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Can chromosomal crossover undo itself?

Can chromosomal crossover undo itself?



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If I have alleles AB on one chromosome and ab on another, and if A and B are far from each other (and also a and b), then there is a lot of chromosomal crossovers happening. If I crossover 7 times, will I end up with the same chromosomes as if I cross over once?


Good thinking. Yes, it is theoretically possible. It is often modelled like this. Have a look at this answer for the maths.

Note however, that to my understanding (and I might be wrong) there is typically either 0 or 1 crossover per pair of chromosomes as cross-over is directly related to the way homologous chromosomes bind together during prophase I of the meiosis by the synapsis. My confusion lies in the fact that, I think, there are sometimes (often?) several synapsis per chromosome pair. Hopefully, someone else will be able to clarify this for us.

As a consequence, the genome-wide recombination rate in humans is almost exactly 23 in humans (Wang et al., 2012). So in practice, such mulitple crossover would very rarely (if ever) happen.


That's quite an interesting question. Crossing over occur during meiosis, there can be more than one in a chromosome indeed. Let's say two crossing over occurs in the same chromosome (the one with your markers A and B), if they both occured in between your markers, you will see no difference. As you said your markers are far from each other you have a good probability to observe that. If your markers were close, your chance to observe a double crossing over is really low.

Also, there is some mechanisms preventing two crossing over to occur too close from each other. I can't tell you exactly what it is about. There is a type of Crossing over not subject to this rule though…

Double crossing over can be an issue when working on genetic maps (using crossing over to determine the order of marker on map). As if this occur we have no way to choose between 0 crossing over or 2 crossing over (meaning markers are actually far from each other.

If you want more explanation about this wide topic, I would suggest you to read this scientific work. They are working on removing inhibition for crossing over and achieve to multiply the number of crossing over by 9 in Arabiodpsis!


Synapsis is the pairing of homologous chromosomes, one from each parent. Crossover occurs following synapsis. The points at which crossover occurs are called chiasmata, and appear to be genetically determined. However, it seems that they are not always at the same locations on homologous chromosomes from different individuals.

That said, the likelihood of crossover being reversed on one chromosome would depend on a series of lucky coincidences and some serious inbreeding, but could conceivably happen. For crossover to be reversed on all chromosomes would be staggeringly unlikely.


Transposable element

A transposable element (TE, transposon, or jumping gene) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. [1] Transposition often results in duplication of the same genetic material. Barbara McClintock's discovery of them earned her a Nobel Prize in 1983. [2]

Transposable elements make up a large fraction of the genome and are responsible for much of the mass of DNA in a eukaryotic cell. Although TEs are selfish genetic elements, many are important in genome function and evolution. [3] Transposons are also very useful to researchers as a means to alter DNA inside a living organism.

There are at least two classes of TEs: Class I TEs or retrotransposons generally function via reverse transcription, while Class II TEs or DNA transposons encode the protein transposase, which they require for insertion and excision, and some of these TEs also encode other proteins. [4]


Contents

In a cell, DNA replication begins at specific locations in the genome, called "origins". Unwinding of DNA at the origin, and synthesis of new strands, forms a replication fork. In addition to DNA polymerase, the enzyme that synthesizes the new DNA by adding nucleotides matched to the template strand, a number of other proteins are associated with the fork and assist in the initiation and continuation of DNA synthesis. DNA replication can also be performed in vitro (outside a cell). DNA polymerases, isolated from cells, and artificial DNA primers are used to initiate DNA synthesis at known sequences in a template molecule. The polymerase chain reaction (PCR), a common laboratory technique, employs such artificial synthesis in a cyclic manner to amplify a specific target DNA fragment from a pool of DNA. [1]

Leading strand Edit

The leading strand template is the template strand of the DNA double helix that is oriented in a 3' to 5' manner. All DNA synthesis occurs 5'-3'. The original DNA strand must be read 3'-5' to produce a 5'-3' nascent strand. The leading strand is formed along the leading strand template as a polymerase "reads" the template DNA and continuously adds nucleotides to the 3' end of the elongating strand. This polymerase is DNA polymerase III (DNA Pol III) in prokaryotes and presumably Pol ε in eukaryotes.

Lagging strand Edit

The lagging strand template is the coding strand of the DNA double helix that is oriented in a 5' to 3' manner. The newly made lagging strand still is synthesized 5'-3'. However, since the DNA is oriented in a manner that does not allow continual synthesis, only small sections can be read at a time. An RNA primer is placed on the DNA strand 3' to the origin of replication. Just as before, DNA Polymerase reads 3'-5' on the original DNA to produce a 5'-3' nascent strand. Polymerase reaches the origin of replication and stops replication until a new RNA primer is placed 3' to the last RNA primer. These fragments of DNA produced on the lagging strand are called Okazaki fragments. The orientation of the original DNA on the lagging strand prevents continual synthesis. As a result, replication of the lagging strand is more complicated than of the leading strand. On the lagging strand template, primase "reads" the DNA and adds RNA to it in short, separated segments. In eukaryotes, primase is intrinsic to Pol α. DNA polymerase III or Pol δ lengthens the primed segments, forming Okazaki fragments. Primer removal in eukaryotes is also performed by Pol δ. In prokaryotes, DNA polymerase I "reads" the fragments, removes the RNA using its flap endonuclease domain, and replaces the RNA nucleotides with DNA nucleotides (this is necessary because RNA and DNA use slightly different kinds of nucleotides). DNA ligase joins the fragments together.

Okazaki fragment Edit

An Okazaki fragment is a relatively short fragment of DNA (with no RNA primer at the 5' terminus) created on the lagging strand during DNA replication. The lengths of Okazaki fragments are between 1,000 and 2,000 nucleotides long in E. coli and are generally between 100 and 200 nucleotides long in eukaryotes. It was originally discovered in 1968 by Reiji Okazaki, Tsuneko Okazaki, and their colleagues while studying replication of bacteriophage DNA in Escherichia coli. [2] [3]

Rate of replication Edit

The rate of DNA replication in a living cell was first measured as the rate of phage T4 DNA elongation in phage-infected E. coli. [4] During the period of exponential DNA increase at 37 °C, the rate was 749 nucleotides per second. The mutation rate per base pair per replication during phage T4 DNA synthesis is 1.7 per 10 8 . [5] Thus semiconservative DNA replication is both rapid and accurate.

Classification of DNA polymerase Edit

Based on sequence homology, DNA polymerases are subdivided into seven different families: A, B, C, D, X, Y, and RT.

1.Family A Polymerases contain both replicative and repair polymerases. Replicative members from this family include the extensively-studied T7 DNA polymerase, as well as the eukaryotic mitochondrial DNA Polymerase γ. Among the repair polymerases are Escherichia coli DNA pol I, Thermus aquaticus pol I, and Bacillus stearothermophilus pol I. These repair polymerases are involved in excision repair and processing of Okazaki fragments generated during lagging strand synthesis.

2.Family B In XPV patients, alternative error-prone polymerases, e.g., Pol ζ (zeta) (polymerase ζ is a B Family polymerase a complex of the catalytic subunit REV3L with Rev7, which associates with Rev1), are thought to be involved in mistakes that result in the cancer predisposition of these patients. The DNA polymerase which belongs to B family contain DTDS motif. The other members are Pol ε, Pol α, Pol δ.

3.Family C Polymerases are the primary bacterial chromosomal replicative enzymes. DNA Polymerase III alpha subunit from E. coli is the catalytic subunit and possesses no known nuclease activity. A separate subunit, the epsilon subunit, possesses the 3'-5' exonuclease activity used for editing during chromosomal replication. Recent research has classified Family C polymerases as a subcategory of Family X.

4.Family D Polymerases are still not very well characterized. All known examples are found in the Euryarchaeota subdomain of Archaea and are thought to be replicative polymerases.

5.Family X Contains the well-known eukaryotic polymerase pol β, as well as other eukaryotic polymerases such as pol σ, pol λ, pol μ, and terminal deoxynucleotidyl transferase (TdT). Pol β is required for short-patch base excision repair, a DNA repair pathway that is essential for repairing abasic sites. Pol λ and Pol μ are involved in non-homologous end-joining, a mechanism for rejoining DNA double-strand breaks. TdT is expressed only in lymphoid tissue, and adds "n nucleotides" to double-strand breaks formed during V(D)J recombination to promote immunological diversity. The yeast Saccharomyces cerevisiae has only one Pol X polymerase, Pol IV, which is involved in non-homologous end-joining.

6.Family Y Y Polymerases differ from others in having a low fidelity on undamaged templates and in their ability to replicate through damaged DNA. Members of this family are hence called translesion synthesis (TLS) polymerases. Depending on the lesion, TLS polymerases can bypass the damage in an error-free or error-prone fashion, the latter resulting in elevated mutagenesis. Xeroderma pigmentosum variant (XPV) patients for instance have mutations in the gene encoding Pol η (eta), which is error-free for UV-lesions. Other members in humans are Pol ι (iota), Pol κ (kappa), and Rev1 (terminal deoxycytidyl transferase). In E. coli, two TLS polymerases, Pol IV (DINB) and Pol V (UmuD'2C), are known.

7.Family RT (reverse transcriptase) The reverse transcriptase family contains examples from both retroviruses and eukaryotic polymerases. The eukaryotic polymerases are usually restricted to telomerases. These polymerases use an RNA template to synthesize the DNA strand.

The Meselson and Stahl experiment was an experiment by Matthew Meselson and Franklin Stahl in 1958 which supported the hypothesis that DNA replication was semiconservative. Semiconservative replication means that when the double stranded DNA helix was replicated, each of the two double stranded DNA helices consisted of one strand coming from the original helix and one newly synthesized. It has been called "the most beautiful experiment in biology. [6] "

Three hypotheses had been previously proposed for the method of replication of DNA.

In the semiconservative hypothesis, proposed by Watson and Crick, the two strands of a DNA molecule separate during replication. Each strand then acts as a template for synthesis of a new strand. [7]

The conservative hypothesis proposed that the entire DNA molecule acted as a template for synthesis of an entirely new one. According to this model, histone proteins bound to the DNA, distorting it in such a way as to expose both strands' bases for hydrogen bonding. [8]

The dispersive hypothesis is exemplified by a model proposed by Max Delbrück, which attempts to solve the problem of unwinding the two strands of the double helix by a mechanism that breaks the DNA backbone every 10 nucleotides or so, untwists the molecule, and attaches the old strand to the end of the newly synthesized one. This would synthesize the DNA in short pieces alternating from one strand to the other. [9]

Each of these three models makes a different prediction about the distribution of the "old" DNA in molecules formed after replication. In the conservative hypothesis, after replication, one molecule is the entirely conserved "old" molecule, and the other is all newly synthesized DNA. The semiconservative hypothesis predicts that each molecule after replication will contain one old and one new strand. The dispersive model predicts that each strand of each new molecule will contain a mixture of old and new DNA. [10]

The semi-conservative theory can be confirmed by making use of the fact that DNA is made up of nitrogen bases. Nitrogen has an isotope N15 (N14 is the most common isotope) called heavy nitrogen. The experiment that confirms the predictions of the semi-conservative theory [11] [12] makes use of this isotope and runs as follows: Bacterial (E coli) DNA is placed in a media containing heavy nitrogen(N15), which binds to the DNA, making it identifiable. Bacteria containing this DNA are then placed in a media with the presence of N14 and left to replicate only once. The new bases will contain nitrogen 14 while the originals will contain N15 The DNA is placed in test tubes containing caesium chloride (heavy compound) and centrifuged at 40,000 revolutions per minute. The caesium chloride molecules sink to the bottom of the test tubes creating a density gradient. The DNA molecules will position at their corresponding level of density (taking into account that N15 is more dense than N14) These test tubes are observed under ultraviolet rays. DNA appears as a fine layer in the test tubes at different heights according to their density. According to the semi-conservative theory, after one replication of DNA, we should obtain 2 hybrid (part N14 part N15) molecules from each original strand of DNA. This would appear as a single line in the test tube. This result would be the same for the dispersive theory. On the other hand, according to the conservative theory, we should obtain one original DNA duplex and a completely new one i.e. two fine lines in the test tube placed separately one from the other. Up to this point, either the semi-conservative or the dispersive theories could be truthful, as experimental evidence confirmed that only one line appeared after one replication. In order to conclude between those two, DNA had to be left to replicate again, still in a media containing N14. In the dispersive theory, after 2 divisions we should obtain a single line, but further up in the test tube, as the DNA molecules become less dense as N14 becomes more abundant in the molecule According to the semi-conservative theory, 2 hybrid molecules and 2 fully N14 molecules should be produced, so two fine lines at different heights in the test tubes should be observed. Experimental evidence confirmed that two lines were observed therefore offering compelling evidence for the semi-conservative theory.

An independent 'genetic' evidence for the semi-conservative theory was provided more recently by high throughput genomic sequencing of individual mutagenized bacteria. E. coli were treated with Ethyl methanesulfonate (EMS), known to induce G:C → A:T transitions due to generation of abnormal base O-6-ethylguanine, which is further misrecognized during DNA replication and paired with T instead of C. The sequenced DNA from individual colonies of EMS-mutagenized bacteria exhibited long stretches of solely G → A or C → T transitions, which in some cases were spanning entire bacterial genome. The elementary explanation of this observation is based on semi-conservative mechanism: one should expect the segregation between daughter strands into different cells after replication, which leads to each descendant cell having exclusively G → A or C → T conversions.

Nitrogen is a major constituent of DNA. 14 N is by far the most abundant isotope of nitrogen, but DNA with the heavier (but non-radioactive) 15 N isotope is also functional.

E. coli were grown for several generations in a medium with 15 N. When DNA is extracted from these cells and centrifuged on a salt density gradient, the DNA separates out at the point at which its density equals that of the salt solution. The DNA of the cells grown in 15 N medium had a higher density than cells grown in normal 14 N medium. After that, E. coli cells with only 15 N in their DNA were transferred to a 14 N medium and were allowed to divide the progress of cell division was monitored by measuring the optical density of the cell suspension.

DNA was extracted periodically and was compared to pure 14 N DNA and 15 N DNA. After one replication, the DNA was found to have close to the intermediate density. Since conservative replication would result in equal amounts of DNA of the higher and lower densities (but no DNA of an intermediate density), conservative replication was excluded. However, this result was consistent with both semiconservative and dispersive replication. Semiconservative replication would result in double-stranded DNA with one strand of 15 N DNA, and one of 14 N DNA, while dispersive replication would result in double-stranded DNA with both strands having mixtures of 15 N and 14 N DNA, either of which would have appeared as DNA of an intermediate density.

The authors continued to sample cells as replication continued. DNA from cells after two replications had been completed was found to consist of equal amounts of DNA with two different densities, one corresponding to the intermediate density of DNA of cells grown for only one division in 14 N medium, the other corresponding to DNA from cells grown exclusively in 14 N medium. This was inconsistent with dispersive replication, which would have resulted in a single density, lower than the intermediate density of the one-generation cells, but still higher than cells grown only in 14 N DNA medium, as the original 15 N DNA would have been split evenly among all DNA strands. The result was consistent with the semiconservative replication hypothesis [11]

DNA replication in prokaryotes is extensively studied in E. coli. It is bi-directional and originates at a single origin of replication (OriC).

Primase Edit

In bacteria, primase binds to the DNA helicase forming a complex called the primosome. Primase is activated by DNA helicase where it then synthesizes a short RNA primer approximately 11 ±1 nucleotides long, to which new nucleotides can be added by DNA polymerase.

Primosome Edit

A primosome is a protein complex responsible for creating RNA primers on single stranded DNA during DNA replication.Primosomes are nucleoproteins assemblies that activate DNA replication forks. Their primary role is to recruit the replicative helicase onto single-stranded DNA. The "replication restart" primosome, defined in Escherichia coli, is involved in the reactivation of arrested replication forks.

Assembly of the Escherichia coli primosome requires six proteins, PriA, PriB, PriC, DnaB, DnaC, and DnaT, acting at a primosome assembly site (pas) on an SSBcoated single-stranded (8s) DNA. Assembly is initiated by interactions of PriA and PriB with ssDNA and the pas. PriC, DnaB, DnaC, and DnaT then act on the PriAPriB- DNA complex to yield the primosome.

The primosome consists of seven proteins: DnaG primase, DnaB helicase, DnaC helicase assistant, DnaT, PriA, Pri B, and PriC. The primosome is utilized once on the leading strand of DNA and repeatedly, initiating each Okazaki fragment, on the lagging DNA strand. Initially the complex formed by PriA, PriB, and PriC binds to DNA. Then the DnaB-DnaC helicase complex attaches along with DnaT. This structure is referred to as the pre-primosome. Finally, DnaG will bind to the pre-primosome forming a complete primosome. The primosome attaches 1-10 RNA nucleotides to the single stranded DNA creating a DNA-RNA hybrid. This sequence of RNA is used as a primer to initiate DNA polymerase III. The RNA bases are ultimately replaced with DNA bases by RNase H nuclease (eukaryotes) or DNA polymerase I nuclease (prokaryotes). DNA Ligase then acts to join the two ends together.

Elongation of DNA strand Edit

Once priming is complete, DNA polymerase III holoenzyme is loaded into the DNA and replication starts. The catalytic mechanism of DNA polymerase III involves the use of two metal ions in the active site, and a region in the active site that can discriminate between deoxyribonucleotides and ribonucleotides. The metal ions are general divalent cations that help the 3' OH initiate a nucleophilic attack onto the alpha phosphate of the deoxyribonucleotide and orient and stabilize the negatively charged triphosphate on the deoxyribonucleotide. Nucleophilic attack by the 3' OH on the alpha phosphate releases pyrophosphate, which is then subsequently hydrolyzed (by inorganic phosphatase) into two phosphates. This hydrolysis drives DNA synthesis to completion.

Furthermore, DNA polymerase III must be able to distinguish between correctly paired bases and incorrectly paired bases. This is accomplished by distinguishing Watson-Crick base pairs through the use of an active site pocket that is complementary in shape to the structure of correctly paired nucleotides. This pocket has a tyrosine residue that is able to form van der Waals interactions with the correctly paired nucleotide. In addition, dsDNA (double stranded DNA) in the active site has a wider and shallower minor groove that permits the formation of hydrogen bonds with the third nitrogen of purine bases and the second oxygen of pyrimidine bases. Finally, the active site makes extensive hydrogen bonds with the DNA backbone. These interactions result in the DNA polymerase III closing around a correctly paired base. If a base is inserted and incorrectly paired, these interactions could not occur due to disruptions in hydrogen bonding and van der Waals interactions.

DNA is read in the 3' → 5' direction, therefore, nucleotides are synthesized (or attached to the template strand) in the 5' → 3' direction. However, one of the parent strands of DNA is 3' → 5' while the other is 5' → 3'. To solve this, replication occurs in opposite directions. Heading towards the replication fork, the leading strand is synthesized in a continuous fashion, only requiring one primer. On the other hand, the lagging strand, heading away from the replication fork, is synthesized in a series of short fragments known as Okazaki fragments, consequently requiring many primers. The RNA primers of Okazaki fragments are subsequently degraded by RNAse H and DNA Polymerase I (exonuclease), and the gap (or nicks) are filled with deoxyribonucleotides and sealed by the enzyme ligase. [13]

Termination Edit

Termination of DNA replication in E. coli is completed through the use of termination sequences and the Tus protein. Tus is a sequence-specific DNA binding protein that promotes termination in prokaryotic DNA replication. In E. Coli, Tus binds to ten closely related 23 basepair binding sites encoded in the bacterial chromosome. These sites, called Ter sites, are designated TerA, TerB, . TerJ. The binding sites are asymmetric, such that when a Tus-Ter complex (Tus protein bound to a Ter site) is encountered by a replication fork from one direction, the complex is dissociated and replication continues (permissive). When encountered from the other direction, however, the Tus-Ter complex provides a much larger kinetic barrier and halts replication (non-permissive). The multiple Ter sites in the chromosome are oriented such that the two oppositely moving replication forks are both stalled in the desired termination region.

In Prokaryotic there are 5 kind of DNA polymerases:

Pol I: implicated in DNA repair has 5'->3' polymerase activity, and both 3'->5' exonuclease activity (proofreading) and 5'->3' exonuclease activity (RNA primer removal).

Pol II: involved in repairing damaged DNA has 3'->5' exonuclease activity.The enzyme is 90 kDa in size and is coded by the polB gene. DNA Pol II can synthesize DNA new base pairs at an average rate of between 40 and 50 nucleotides/second.

Pol III: the main polymerase in bacteria (responsible for elongation) has 3'->5' exonuclease activity (proofreading).The replisome is composed of the following: 2 DNA Pol III enzymes, made up of α, ε and θ subunits. the α subunit synthesizes the RNA/DNA primer. the ε subunit synthesizes the leading strand. the θ subunit stimulates the ε subunit's proofreading. 2 β units which act as sliding DNA clamps, they keep the polymerase bound to the DNA. 2 τ units which acts to dimerize two of the core enzymes (α, ε, and θ subunits). 1 γ unit which acts as a clamp loader for the lagging strand Okazaki fragments, helping the two β subunits to form a unit and bind to DNA. The γ unit is made up of 5 γ subunits which include 3 γ subunits, 1 δ subunit, and 1 δ' subunit. The δ is involved in copying of the lagging strand

Pol IV: a Y-family DNA polymerase.

Pol V: a Y-family DNA polymerase participates in bypassing DNA damage.

DNA Polymerase I or Pol I Edit

DNA Polymerase I (or Pol I) is an enzyme that participates in the process of DNA replication in prokaryotes. It contains 928 amino acids, and is an example of a processive enzyme - it can sequentially catalyze multiple polymerisations. It was Discovered by Arthur Kornberg in 1956, it was the first known DNA polymerase (and, indeed, the first known of any kind of polymerase). It was initially characterized in E. coli, although it is ubiquitous in prokaryotes. In E. coli and many other bacteria, the gene which encodes Pol I is known as polA. Pol I possesses three enzymatic activities: (1) a 5' -> 3' (forward) DNA polymerase activity, requiring a 3' primer site and a template strand (2) a 3' -> 5' (reverse) exonuclease activity that mediates proofreading and (3) a 5' -> 3' (forward) exonuclease activity mediating nick translation during DNA repair.

Klenow fragment Edit

The 5' → 3' exonuclease activity of DNA polymerase I from E. coli makes it unsuitable for many applications, the Klenow fragment, which lacks this activity, can be very useful in research. The Klenow fragment is extremely useful for research-based tasks such as: (1) Synthesis of double-stranded DNA from single-stranded templates (2) Filling in (meaning removal of overhangs to create blunt ends) recessed 3' ends of DNA fragments (3) Digesting away protruding 3' overhangs (4) Preparation of radioactive DNA probes. The Klenow fragment was also the original enzyme used for greatly amplifying segments of DNA in the polymerase chain reaction (PCR) process, before being replaced by thermostable enzymes such as Taq polymerase.

Many cellular processes (DNA replication, transcription, translation, recombination, DNA repair, ribosome biogenesis) involve the separation of nucleic acid strands. Helicases are often utilized to separate strands of a DNA double helix or a self-annealed RNA molecule using the energy from ATP hydrolysis, a process characterized by the breaking of hydrogen bonds between annealed nucleotide bases. They move incrementally along one nucleic acid strand of the duplex with a directionality and processivity specific to each particular enzyme. There are many helicases (14 confirmed in E. coli, 24 in human cells) resulting from the great variety of processes in which strand separation must be catalyzed.

Helicases adopt different structures and oligomerization states. Whereas DnaB-like helicases unwind DNA as donut-shaped hexamers, other enzymes have been shown to be active as monomers or dimers. Studies have shown that helicases may act passively, waiting for uncatalyzed unwinding to take place and then translocating between displaced strands,[1] or can play an active role in catalyzing strand separation using the energy generated in ATP hydrolysis. In the latter case, the helicase acts comparably to an active motor, unwinding and translocating along its substrate as a direct result of its ATPase activity. Helicases may process much faster in vivo than in vitro due to the presence of accessory proteins that aid in the destabilization of the fork junction. Defects in the gene that codes helicase cause Werner syndrome, a disorder characterized by the appearance of premature aging. [14]

Helicases have been classified in 5 superfamilies (SF1-SF5). All of the proteins bind ATP, and, as a consequence, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs.

Superfamily I: UvrD (E. coli, DNA repair), Rep (E. coli, DNA replication), PcrA (Staphylococcus aureus, recombination), Dda (bacteriophage T4, replication initiation), RecD (E. coli, recombinational repair), TraI (F-plasmid, conjugative DNA transfer). This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in positive-strand single-stranded RNA viruses from superfamily 1. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.

Superfamily II: RecQ (E. coli, DNA repair), eIF4A (Baker's Yeast, RNA translation), WRN (human, DNA repair), NS3[5] (Hepatitis C virus, replication). TRCF (Mfd) (E.coli, transcription-repair coupling).

Superfamily III: LTag (Simian Virus 40, replication), E1 (human papillomavirus, replication), Rep (Adeno-Associated Virus, replication, viral integration, virion packaging). Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses.[6][7] Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori, and the viral DNA is replicated.

DnaB-like family: dnaB (E. coli, replication), gp41 (bacteriophage T4, DNA replication), T7gp4 (bacteriophage T7, DNA replication).

Rho-like family: Rho (E. coli, transcription termination). Note that these superfamilies do not subsume all possible helicases. For example, XPB and ERCC2 are helicases not included in any of the above families.

RNA Helicases RNA Helicases and DNA Helicases can be found together in all the Helicase Super Families except for SF6. [15] However, not all RNA Helicases exhibit helicase activity as defined by enzymatic function, i.e., proteins of the Swi/Snf family. Although these proteins carry the typical helicase motifs, hydrolize ATP in a nucleic acid-dependent manner, and are built around a helicase core, in general, no unwinding activity is observed. [16]

RNA Helicases that do exhibit unwinding activity have been characterized by at least two different mechanisms: canonical duplex unwinding and local strand separation. Canonical duplex unwinding is the stepwise directional separation of a duplex strand, as described above, for DNA unwinding. However, local strand separation occurs by a process wherein the helicase enzyme is loaded at any place along the duplex. This is usually aided by a single-stranded region of the RNA, and the loading of the enzyme is accompanied with ATP binding. [17] Once the helicase and ATP are bound, local strand separation occurs, which requires binding of ATP but not the actual process of ATP hydrolysis. [18] Presented with fewer base pairs the duplex then dissociates without further assistance from the enzyme. This mode of unwinding is used by DEAD-box helicases. [19]

Topoisomerases are enzymes that unwind and wind DNA, in order for DNA to control the synthesis of proteins, and to facilitate DNA replication. The double-helical configuration that DNA strands naturally reside in makes them difficult to separate, and yet they must be separated by helicase proteins if other enzymes are to transcribe the sequences that encode proteins, or if chromosomes are to be replicated. In so-called circular DNA, in which double helical DNA is bent around and joined in a circle, the two strands are topologically linked, or knotted. Otherwise, identical loops of DNA having different numbers of twists are topoisomers, and cannot be interconverted by any process that does not involve the breaking of DNA strands. Topoisomerases catalyze and guide the unknotting or unkinking of DNA[3] by creating transient breaks in the DNA using a conserved Tyrosine as the catalytic residue. The insertion of viral DNA into chromosomes and other forms of recombination can also require the action of topoisomerases.

Topoisomerases can fix these topological problems and are separated into two types separated by the number of strands cut in one round of action: [20] Both these classes of enzyme utilize a conserved tyrosine. However these enzymes are structurally and mechanistically different.

    cuts one strand of a DNA double helix, relaxation occurs, and then the cut strand is reannealed. Cutting one strand allows the part of the molecule on one side of the cut to rotate around the uncut strand, thereby reducing stress from too much or too little twist in the helix. Such stress is introduced when the DNA strand is "supercoiled" or uncoiled to or from higher orders of coiling. Type I topoisomerases are subdivided into two subclasses: type IA topoisomerases, which share many structural and mechanistic features with the type II topoisomerases, and type IB topoisomerases, which utilize a controlled rotary mechanism. Examples of type IA topoisomerases include topo I and topo III. In the past, type IB topoisomerases were referred to as eukaryotic topo I, but IB topoisomerases are present in all three domains of life. It is interesting to note that type IA topoisomerases form a covalent intermediate with the 5' end of DNA, while the IB topoisomerases form a covalent intermediate with the 3' end of DNA. Recently, a type IC topoisomerase has been identified, called topo V. While it is structurally unique from type IA and IB topoisomerases, it shares a similar mechanism with type IB topoisomerase. cuts both strands of one DNA double helix, passes another unbroken DNA helix through it, and then reanneals the cut strand. It is also split into two subclasses: type IIA and type IIB topoisomerases, which share similar structure and mechanisms. Examples of type IIA topoisomerases include eukaryotic topo II, E. coli gyrase, and E. coli topo IV. Examples of type IIB topoisomerase include topo VI.

Both type I and type II topoisomerases change the linking number (L) of DNA. Type IA topoisomerases change the linking number by one, type IB and type IC topoisomerases change the linking number by any integer, while type IIA and type IIB topoisomerases change the linking number by two.

Many drugs operate through interference with the topoisomerases. The broad-spectrum fluoroquinolone antibiotics act by disrupting the function of bacterial type II topoisomerases. Some chemotherapy drugs work by interfering with topoisomerases in cancer cells: type 1 is inhibited by irinotecan and topotecan. type 2 is inhibited by etoposide (VP-16), teniposide and HU-331, a quinolone synthesized from cannabidiol. Topoisomerase I is the antigen recognized by Anti Scl-70 antibodies in scleroderma. These small molecule inhibitors act as efficient anti-bacterial and anti-cancer agents by hijacking the natural ability of topoisomerase to create breaks in chromosomal DNA. These breaks in DNA accumulate, ultimately leading to programmed cell death, or apoptosis.

DNA replication in eukaryotes is much more complicated than in prokaryotes, although there are many similar aspects. Eukaryotic cells can only initiate DNA replication at a specific point in the cell cycle, the beginning of S phase.

DNA replication in eukaryotes occurs only in the S phase of the cell cycle. However, pre-initiation occurs in the G1 phase. Thus, the separation of pre-initiation and activation ensures that the origin can only fire once per cell cycle. Due to the sheer size of chromosomes in eukaryotes, eukaryotic chromosomes contain multiple origins of replication. Some origins are well characterized, such as the autonomously replicating sequences (ARS) of yeast while other eukaryotic origins, particularly those in metazoa, can be found in spans of thousands of basepairs. [21]

Eukaryotic DNA polymerase Edit

There are at least 15 known Eukaryotic DNA polymerase:

POLA1, POLA2: Pol α (also called RNA primase): forms a complex with a small catalytic (PriS) and a large noncatalytic (PriL) subunit, with the Pri subunits acting as a primase (synthesizing an RNA primer), and then with DNA Pol α elongating that primer with DNA nucleotides. After around 20 nucleotides[3] elongation is taken over by Pol ε (on the leading strand) and δ (on the lagging strand).

POLB: Pol β: Implicated in repairing DNA, in base excision repair and gap-filling synthesis.

POLG, POLG2: Pol γ: Replicates and repairs mitochondrial DNA and has proofreading 3'->5' exonuclease activity.

POLD1, POLD2, POLD3, POLD4: Pol δ: Highly processive and has proofreading 3'->5' exonuclease activity. Thought to be the main polymerase involved in lagging strand synthesis, though there is still debate about its role.

POLE, POLE2, POLE3: Pol ε: Also highly processive and has proofreading 3'->5' exonuclease activity. Highly related to pol δ, and thought to be the main polymerase involved in leading strand synthesis[5], though there is again still debate about its role.

POLH, POLI, POLK, : η, ι, κ, and Rev1 are Y-family DNA polymerases and Pol ζ is a B-family DNA polymerase. These polymerases are involved in the bypass of DNA damage.

There are also other eukaryotic polymerases known, which are not as well characterized: POLQ: 'θ POLL: λ φ σ POLM: μ None of the eukaryotic polymerases can remove primers (5'->3' exonuclease activity) that function is carried out by other enzymes. Only the polymerases that deal with the elongation (γ, δ and ε) have proofreading ability (3'->5' exonuclease).

Preparation in G1 phase

The first step in DNA replication is the formation of the pre-initiation replication complex (the pre-RC). The formation of this complex occurs in two stages. The first stage requires that there is no CDK activity. This can only occur in early G1. The formation of the pre-RC is known as licensing, but a licensed pre-RC cannot initiate replication in the G1 phase Current models hold that it begins with the binding of the origin recognition complex (ORC) to the origin. This complex is a hexamer of related proteins and remains bound to the origin, even after DNA replication occurs. Furthermore, ORC is the functional analogue of prokaryotic DnaA. Following the binding of ORC to the origin, Cdc6/Cdc18 and Cdt1 coordinate the loading of the MCM (Mini Chromosome Maintenance) complex to the origin by first binding to ORC and then binding to the MCM complex. The MCM complex is thought to be the major DNA helicase in eukaryotic organisms. Once binding of MCM occurs, a fully licensed pre-RC exists.

DNA Replication occurs during the S phase Edit

Activation of the complex occurs in S-phase and requires Cdk2-Cyclin E and Ddk. The activation process begins with the addition of Mcm10 to the pre-RC, which displaces Cdt1. Following this, Ddk phosphorylates Mcm3-7, which activates the helicase. It is believed that ORC and Cdc6/18 are phosphorylated by Cdk2-Cyclin E. Ddk and the Cdk complex then recruits another protein called Cdc45, which then recruits all of the DNA replication proteins to the replication fork. At this stage the origin fires and DNA synthesis begins. Activation of a new round of replication is prevented through the actions of the cyclin dependent kinases and a protein known as geminin. Geminin binds to Cdt1 and sequesters it. It is a periodic protein that first appears in S-phase and is degraded in late M-phase, possibly through the action of the anaphase promoting complex (APC). In addition, phosphorylation of Cdc6/18 prevent it from binding to the ORC (thus inhibiting loading of the MCM complex) while the phosphorylation of ORC remains unclear. Cells in the G0 stage of the cell cycle are prevented from initiating a round of replication because the Mcm proteins are not expressed.

At least three different types of eukaryotic DNA polymerases are involved in the replication of DNA in animal cells (POL α, Pol δ and POL ε).

Pol α forms a complex with a small catalytic (PriS) and a large noncatalytic (PriL) subunit, with the Pri subunits acting as a primase (synthesizing an RNA primer), and then with DNA Pol α elongating that primer with DNA nucleotides. After around 20 nucleotides elongation is taken over by Pol ε (on the leading strand) and δ (on the lagging strand).

Pol δ: Highly processive and has proofreading 3'->5' exonuclease activity. Thought to be the main polymerase involved in leading strand synthesis, though there is still debate about its role.

Pol ε: Also highly processive and has proofreading 3'->5' exonuclease activity. Highly related to pol δ, and thought to be the main polymerase involved in lagging strand synthesis, though there is again still debate about its role. [22]

Nuclear and mitochondrial DNA are thought to be of separate evolutionary origin, with the mtDNA being derived from the circular genomes of the bacteria that were engulfed by the early ancestors of today's eukaryotic cells. This theory is called the endosymbiotic theory. Each mitochondrion is estimated to contain 2-10 mtDNA copies. In the cells of extant organisms, the vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA, but the genes for some of them, if not most, are thought to have originally been of bacterial origin, having since been transferred to the eukaryotic nucleus during evolution.

mtDNA is replicated by the DNA polymerase gamma complex which is composed of a 140 kDa catalytic DNA polymerase encoded by the POLG gene and a 55 kDa accessory subunit encoded by the POLG2 gene. During embryogenesis, replication of mtDNA is strictly down-regulated from the fertilized oocyte through the preimplantation embryo. At the blastocyst stage, the onset of mtDNA replication is specific to the cells of the trophectoderm. In contrast, the cells of the inner cell mass restrict mtDNA replication until they receive the signals to differentiate to specific cell types. D-loop replication is a process by which chloroplasts and mitochondria replicate their genetic material. An important component of understanding D-loop replication is that chloroplasts and mitochondria have a single circular chromosome like bacteria instead of the linear chromosomes found in eukaryotes. In many organisms, one strand of DNA in the plastid comprises heavier nucleotides (relatively more purines: adenine and guanine). This strand is called the H (heavy) strand. The L (light) strand comprises lighter nucleotides (pyrimidines: thymine and cytosine). Replication begins with replication of the heavy strand starting at the D-loop (also known as the control region). An origin of replication opens, and the heavy strand is replicated in one direction. After heavy strand replication has continued for some time, a new light strand is also synthesized, through the opening of another origin of replication. When diagramed, the resulting structure looks like the letter D. The D-loop region is important for phylogeographic studies. Because the region does not code for any genes, it is free to vary with only a few selective limitations on size and heavy/light strand factors. The mutation rate is among the fastest of anywhere in either the nuclear or mitochondrial genomes in animals. Mutations in the D-loop can effectively track recent and rapid evolutionary changes such as within species and among very closely related species. [23]

It was first developed and utilized by Roy Britten and his colleagues at the Carnegie Institution of Washington in the 1960s. [24] [25] Of particular note, it was through Cot analysis that the redundant (repetitive) nature of eukaryotic genomes was first discovered. Repeated sequences in DNA. [26] However, it wasn't until the breakthrough DNA reassociation kinetics experiments of Britten and his colleagues that it was shown that not all DNA coded for genes. In fact, their experiments demonstrated that the majority of eukaryotic genomic DNA is composed of repetitive, non-coding elements. The amount of single and double-stranded DNA is measured by rapidly diluting the sample, which slows reassociation, and then binding the DNA to a hydroxylapatite column. The column is first washed with a low concentration of sodium phosphate buffer, which elutes the single-stranded DNA, and then with high concentrations of phosphate, which elutes the double stranded DNA. The amount of DNA in these two solutions is then measured using a spectrophotometer. Since a sequence of single-stranded DNA needs to find its complementary strand to reform a double helix, common sequences renature more rapidly than rare sequences. Indeed, the rate at which a sequence will reassociate is proportional to the number of copies of that sequence in the DNA sample. A sample with a highly-repetitive sequence will renature rapidly, while complex sequences will renature slowly. However, instead of simply measuring the percentage of double-stranded DNA versus time, the amount of renaturation is measured relative to a C0t value. The C0t value is the product of C0 (the initial concentration of DNA), t (time in seconds), and a constant that depends on the concentration of cations in the buffer. Repetitive DNA will renature at low C0t values, while complex and unique DNA sequences will renature at high C0t values.

DNA damage, due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day. While this constitutes only 0.000165% of the human genome's approximately 6 billion bases (3 billion base pairs), unrepaired lesions in critical genes (such as tumor suppressor genes) can impede a cell's ability to carry out its function and appreciably increase the likelihood of tumor formation.

The vast majority of DNA damage affects the primary structure of the double helix that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules' regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable to the effects of DNA damage. [27]

Types of DNA damage Edit

There are five main types of damage to DNA due to endogenous cellular processes: (1) oxidation of bases [e.g. 8-oxo-7,8-dihydroguanine (8-oxoG)] and generation of DNA strand interruptions from reactive oxygen species (2) alkylation of bases (usually methylation), such as formation of 7-methylguanine, 1-methyladenine, 6-O-Methylguanine (3) hydrolysis of bases, such as deamination, depurination, and depyrimidination (4) "bulky adduct formation" (i.e., benzo[a]pyrene diol epoxide-dG adduct) (5) mismatch of bases, due to errors in DNA replication, in which the wrong DNA base is stitched into place in a newly forming DNA strand, or a DNA base is skipped over or mistakenly inserted. Damage caused by exogenous agents Damage caused by exogenous agents comes in many forms. Some examples are described below.

UV-B light causes crosslinking between adjacent cytosine and thymine bases creating pyrimidine dimers. This is called direct DNA damage.

UV-A light creates mostly free radicals. The damage caused by free radicals is called indirect DNA damage.

Ionizing radiation such as that created by radioactive decay or in cosmic rays causes breaks in DNA strands. Low-level ionizing radiation may induce irreparable DNA damage (leading to replicational and transcriptional errors needed for neoplasia or may trigger viral interactions) leading to pre-mature aging and cancer.

Thermal disruption at elevated temperature increases the rate of depurination (loss of purine bases from the DNA backbone) and single-strand breaks. For example, hydrolytic depurination is seen in the thermophilic bacteria, which grow in hot springs at 40-80 °C. The rate of depurination (300 purine residues per genome per generation) is too high in these species to be repaired by normal repair machinery, hence a possibility of an adaptive response cannot be ruled out.

Industrial chemicals also play very important role in DNA damage, such as vinyl chloride and hydrogen peroxide, and environmental chemicals such as polycyclic hydrocarbons found in smoke, soot and tar create a huge diversity of DNA adducts- ethenobases, oxidized bases, alkylated phosphotriesters and Crosslinking of DNA just to name a few. UV damage, alkylation/methylation, X-ray damage and oxidative damage are examples of induced damage. Spontaneous damage can include the loss of a base, deamination, sugar ring puckering and tautomeric shift.

Sources of damage Edit

DNA damage can be subdivided into two main types:

Endogenous damage such as attack by reactive oxygen species produced from normal metabolic byproducts, especially the process of oxidative deamination, and this also includes base mismatches due to replication errors

Exogenous damage caused by external agents such as

ultraviolet [UV 200-300 nm] radiation from the sun

other radiation frequencies, including x-rays and gamma rays

hydrolysis or thermal disruption

human-made mutagenic chemicals, especially aromatic compounds that act as DNA intercalating agents

cancer chemotherapy and radiotherapy

Types of mutation Edit

When DNA damages are repaired this can sometimes give rise to a simple one base-pair mutation, described here. (Deletions and translocations can also arise during repair)

Transition In molecular biology, a transition is a point mutation that changes a purine nucleotide to another purine (A ↔ G) or a pyrimidine nucleotide to another pyrimidine (C ↔ T). Approximately two out of three single nucleotide polymorphisms (SNPs) are transitions. Transitions can be caused by oxidative deamination and tautomerization. Although there are twice as many possible transversions, transitions appear more often in genomes, possibly due to the molecular mechanisms that generate them. 5-Methylcytosine is more prone to transition than unmethylated cytosine, due to spontaneous deamination. This mechanism is important because it dictates the rarity of CpG islands.

Transversion In molecular biology, transversion refers to the substitution of a purine for a pyrimidine or vice versa. It can only be reverted by a spontaneous reversion. Because this type of mutation changes the chemical structure dramatically, the consequences of this change tend to be more severe and less common than that of transitions. Transversions can be caused by ionizing radiation and alkylating agents.

Defects in the NER mechanism are responsible for squally several genetic disorders, including:

Xeroderma pigmentosum: hypersensitivity to sunlight/UV, resulting in increased skin cancer incidence and premature aging

Cockayne syndrome: hypersensitivity to UV and chemical agents

Trichothiodystrophy: sensitive skin, brittle hair and nails Mental retardation often accompanies the latter two disorders, suggesting increased vulnerability of developmental neurons.

Other DNA repair disorders include:

Werner's syndrome: premature aging and retarded growth

Bloom's syndrome: sunlight hypersensitivity, high incidence of malignancies (especially leukemias).

Ataxia telangiectasia: sensitivity to ionizing radiation and some chemical agents

All of the above diseases are often called "segmental progerias" ("accelerated aging diseases") because their victims appear elderly and suffer from aging-related diseases at an abnormally young age, while not manifesting all the symptoms of old age.

Other diseases associated with reduced DNA repair function include Fanconi's anemia, hereditary breast cancer and hereditary colon cancer.

Chromosomes can be divided into two types—autosomes, and sex chromosomes. Certain genetic traits are linked to your sex, and are passed on through the sex chromosomes. The autosomes contain the rest of the genetic hereditary information. All act in the same way during cell division. Human cells have 23 pairs of large linear nuclear chromosomes, (22 pairs of autosomes and one pair of sex chromosomes) giving a total of 46 per cell. In addition to these, human cells have many hundreds of copies of the mitochondrial genome. Sequencing of the human genome has provided a great deal of information about each of the chromosomes. Below is a table compiling statistics for the chromosomes, based on the Sanger Institute's human genome information in the Vertebrate Genome Annotation (VEGA) database. Number of genes is an estimate as it is in part based on gene predictions. Total chromosome length is an estimate as well, based on the estimated size of unsequenced heterochromatin regions.

Chromosome Genes Total bases Sequenced bases [28]
1 4,220 247,199,719 224,999,719
2 1,491 242,751,149 237,712,649
3 1,550 199,446,827 194,704,827
4 446 191,263,063 187,297,063
5 609 180,837,866 177,702,766
6 2,281 170,896,993 167,273,993
7 2,135 158,821,424 154,952,424
8 1,106 146,274,826 142,612,826
9 1,920 140,442,298 120,312,298
10 1,793 135,374,737 131,624,737
11 379 134,452,384 131,130,853
12 1,430 132,289,534 130,303,534
13 924 114,127,980 95,559,980
14 1,347 106,360,585 88,290,585
15 921 100,338,915 81,341,915
16 909 88,822,254 78,884,754
17 1,672 78,654,742 77,800,220
18 519 76,117,153 74,656,155
19 1,555 63,806,651 55,785,651
20 1,008 62,435,965 59,505,254
21 578 46,944,323 34,171,998
22 1,092 49,528,953 34,893,953
X (sex chromosome) 1,846 154,913,754 151,058,754
Y (sex chromosome) 454 57,741,652 25,121,652
Total 32,185 3,079,843,747 2,857,698,560

Chromosomal aberrations are disruptions in the normal chromosomal content of a cell and are a major cause of genetic conditions in humans, such as Down syndrome. Some chromosome abnormalities do not cause disease in carriers, such as translocations, or chromosomal inversions, although they may lead to a higher chance of birthing a child with a chromosome disorder. Abnormal numbers of chromosomes or chromosome sets, aneuploidy, may be lethal or give rise to genetic disorders. Genetic counseling is offered for families that may carry a chromosome rearrangement.

The gain or loss of DNA from chromosomes can lead to a variety of genetic disorders. Human examples include:

    , which is caused by the deletion of part of the short arm of chromosome 5. "Cri du chat" means "cry of the cat" in French, and the condition was so-named because affected babies make high-pitched cries that sound like those of a cat. Affected individuals have wide-set eyes, a small head and jaw, moderate to severe mental health issues, and are very short. , usually is caused by an extra copy of chromosome 21 (trisomy 21). Characteristics include decreased muscle tone, stockier build, asymmetrical skull, slanting eyes and mild to moderate developmental disability. [29] , which is the second-most-common trisomy Down syndrome is the most common. It is a trisomy of chromosome 18. Symptoms include motor retardation, developmental disability and numerous congenital anomalies causing serious health problems. Ninety percent die in infancy however, those that live past their first birthday usually are quite healthy thereafter. They have a characteristic clenched hands and overlapping fingers. , abbreviation for Isodicentric 15 on chromosome 15 also called the following names due to various researches, but they all mean the same IDIC(15), Inverted duplication 15, extra Marker, Inv dup 15, partial tetrasomy 15 , also called the terminal 11q deletion disorder. [30] This is a very rare disorder. Those affected have normal intelligence or mild developmental disability, with poor expressive language skills. Most have a bleeding disorder called Paris-Trousseau syndrome. (XXY). Men with Klinefelter syndrome are usually sterile, and tend to have longer arms and legs and to be taller than their peers. Boys with the syndrome are often shy and quiet, and have a higher incidence of speech delay and dyslexia. During puberty, without testosterone treatment, some of them may develop gynecomastia. , also called D-Syndrome or trisomy-13. Symptoms are somewhat similar to those of trisomy-18, but they do not have the characteristic hand shape. . This means there is an extra, abnormal chromosome. Features depend on the origin of the extra genetic material. Cat-eye syndrome and isodicentric chromosome 15 syndrome (or Idic15) are both caused by a supernumerary marker chromosome, as is Pallister-Killian syndrome. (XXX). XXX girls tend to be tall and thin. They have a higher incidence of dyslexia. (X instead of XX or XY). In Turner syndrome, female sexual characteristics are present but underdeveloped. People with Turner syndrome often have a short stature, low hairline, abnormal eye features and bone development and a "caved-in" appearance to the chest. . XYY boys are usually taller than their siblings. Like XXY boys and XXX girls, they are somewhat more likely to have learning difficulties. , which is caused by partial deletion of the short arm of chromosome 4. It is characterized by severe growth retardation and severe to profound mental health issues.

Chromosomal mutations produce changes in whole chromosomes (more than one gene) or in the number of chromosomes present.

  • Deletion – loss of part of a chromosome
  • Duplication – extra copies of a part of a chromosome
  • Inversion – reverse the direction of a part of a chromosome
  • Translocation – part of a chromosome breaks off and attaches to another chromosome

Most mutations are neutral – have little or no effect. Chromosomal aberrations are the changes in the structure of chromosomes. It has a great role in evolution. A detailed graphical display of all human chromosomes and the diseases annotated at the correct spot may be found at the Oak Ridge National Laboratory. [31]

Recombination is a process by which a molecule of nucleic acid (usually DNA, but can also be RNA) is broken and then joined to a different one (or in which genetic information is exchanged between two such molecules). Recombination ordinarily occurs between similar molecules of DNA, as in homologous recombination. Recombination is a common method of DNA repair in both bacteria and eukaryotes. In eukaryotes, recombination also occurs in meiosis, where it facilitates informational exchange and/or chromosomal crossover. The crossover process leads to offspring's having different combinations of genes from those of their parents, and can occasionally produce new chimeric alleles. In organisms with an adaptive immune system, a type of genetic recombination called V(D)J recombination helps immune cells rapidly diversify to recognize and adapt to new pathogens. The shuffling of genes brought about by genetic recombination can have long term advantages, as it is a major engine of genetic variation and also allows sexually reproducing organisms to avoid Muller's ratchet, in which the genomes of an asexual population accumulate deleterious mutations in an irreversible manner. In genetic engineering, recombination can also refer to artificial and deliberate recombination of disparate pieces of DNA, often from different organisms, creating what is called recombinant DNA. A prime example of such a use of genetic recombination is gene targeting, which can be used to add, delete or otherwise change an organism's genes. This technique is important to biomedical researchers as it allows them to study the effects of specific genes. Techniques based on genetic recombination are also applied in protein engineering to develop new proteins of biological interest. [32]

Chromosomal crossover in eukaryotes is an exchange of genetic material between homologous chromosomes. It can occur in one of the final phases of genetic recombination, which occurs during prophase I of meiosis (pachytene). The pairing of homologous chromsomes during meiosis (synapsis) begins before the synaptonemal complex develops, and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome. Crossing over was described, in theory, by Thomas Hunt Morgan. He relied on the discovery of the Belgian Professor Frans Alfons Janssens of the University of Leuven who described the phenomenon in 1909 and had called it 'chiasmatypie'. The term chiasma is linked if not identical to chromosomal crossover. Morgan immediately saw the great importance of Janssens' cytological interpretation of chiasmata to the experimental results of his research on the heredity of Drosophila. The physical basis of crossing over was first demonstrated by Harriet Creighton and Barbara McClintock in 1931.

Meiotic recombination can be initiated by double-stranded breaks that can be introduced into the DNA by the Spo11 protein. In addition, meiotic recombination can be induced in response to spontaneous double strand breaks, possibly caused by reactive oxygen species, carried over from the prior round of synthesis. [33] One or more exonucleases then digest the 5’ ends generated by the double-stranded breaks to produce 3’ single-stranded DNA tails (see lowest Figure in this section). The meiosis-specific recombinase Dmc1 and the general recombinase Rad51 coat the single-stranded DNA to form nucleoprotein filaments.The recombinases catalyze invasion of the opposite chromatid by the single-stranded DNA from one end of the break. Next, the 3’ end of the invading DNA primes DNA synthesis, causing displacement of the complementary strand.

Crossover recombinants are generated by a process in which the displaced complementary strand subsequently anneals to the single-stranded DNA generated from the other end of the initial double-stranded break (see DHJ pathway on the Figure). The structure that results is a cross-strand exchange, also known as a Holliday junction. The contact between two chromatids that will soon undergo crossing-over is known as a chiasma. The Holliday junction is a tetrahedral structure which can be 'pulled' by other recombinases, moving it along the four-stranded structure (see Double Holliday Junction or DHJ in the Figure).

Gene conversion can result from the repair of a double strand break. Gene conversion involves the unidirectional transfer of genetic sequence information from a 'donor' sequence to a highly homologous 'acceptor' chromosome. Gene conversion usually occurs by Synthesis Dependent Strand Annealing (SDSA) [34] [35] [36] illustrated in the lowest Figure in this section. In this model of SDSA DNA repair, a free strand of DNA from the end of a double strand break invades an homologous chromosome, extending itself by replication along the sequence on the complementary strand of DNA of the ‘donor’ chromosome. The extended strand is then retracted from the donor chromosome and pairs with the complementary sequence on the recipient chromosome in a region at the other end of the double strand break (needing about 25 to 50 base pairs of homology). [34] This allows completion of healing of the double strand break by replication, to complete the duplex structure on the recipient chromosome, from information on the extended strand copied from the donor chromosome. The usual length of a gene conversion tract in mammals is between 200 to 1,000 base pairs. [37]

During meiosis, gene conversion is most often associated with non-crossover of outside regions (e.g. the SDSA pathway shown in the Figure). Less frequently, gene conversion during meiosis is associated with crossover of outside regions and these events are usually generated by the DHJ pathway. Gene conversion without crossover occurs more frequently than crossover recombination during meiosis in many organisms, often by about a 2 to 1 ratio. [38] During mitosis, gene conversion is almost the exclusive mode of double strand break repair by homologous recombination. [36]

Studies of gene conversion have contributed to our understanding of the adaptive function of meiotic recombination. Since gene conversion in most species studied is more frequently of the non-crossover type, [38] explanations for the adaptive function of meiotic recombination that focus exclusively on the adaptive benefit of producing new genetic variation seem inadequate to explain the majority of recombination events during meiosis. However, the majority of meiotic recombination events can be explained by the proposal that they are an adaptation for repair of damages in the DNA that is to be passed on to gametes. [39] [40]

Genetic recombination is catalyzed by enzymes called recombinases. RecA, the chief recombinase found in Escherichia coli, is responsible for the repair of DNA double strand breaks (DSBs). In yeast and other eukaryotic organisms there are two recombinases required for repairing DSBs. The RAD51 protein is employed in both mitotic and meiotic recombination, whereas the DMC1 protein is specific to meiotic recombination.

Nonhomologous recombination Recombinational repair can infrequently occur between DNA sequences that contain no or little sequence homology. This is referred to as nonhomologous recombination.


Talk:Genetic recombination

See Muller's ratchet Recombination reduces the degree to which genes in a chromosome are linked. This allows "good" genes to survive and it ensures bad genes do not accumulate within the genome. —The preceding unsigned comment was added by 129.97.248.107 (talk) 08:04, 19 March 2007 (UTC).

It seems imprecise to define recombination as separating genes (this is rather the case with transpositions/translocations). Rather alleles are separated. Sboehringer

Does this article, perhaps, need to be merged (or merged and re-split along better lines) with chromosomal crossover?--ES2 18:31, 24 Jul 2004 (UTC)

This article was distinct until it was butchered on 23 July 2004. That edit eliminated the general definition of genetic recombination and reduced it to being nothing more than chromosomal crossover--which was addressed in the original article. If I weren't too busy to follow up on this right now, I'd probably revert all the way back to 23 July. AdamRetchless 04:23, 20 Jan 2005 (UTC) I didn't think that expanding a stub was exactly butchering the article. Thankfully the article has gotten better since that expansion. --ES2 05:01, 26 April 2006 (UTC)

I also think these two articles can be merged - unless someone can make the case that crossover and recombination refer to fundamentally different processes. Dr d12 20:55, 9 December 2006 (UTC)

I have a real problem with the use of intra- vs inter-chromosomal recombination here. Ben Carritt 17:48, 23 December 2005 (UTC)

Cre is a type of Recombinase (read Cyclic Recombinase)which has been found in the Bacteriophage P1. Cre catalyses a reaction between two 'Lox P' (read Loci of X over P1) sites, which are 34 bp sequences, causing splicing of the gene which is flanked by these two Lox P sites, leaving behind just the Lox site. This system is called the Cre-Lox system and has been used in effectively studying Mutations, allelic variations and is currently being used by the Biotechnolgy industry in producing trasgenic species of mice and plants to derive useful biological products. Bold text

Does recombination create new alleles, or does it keep the current ones intact? 5th April 2006

Recombination does not respect reading frame boundaries, and therefore can produce novel alleles. One research article describing this says: The asymmetric patterns of polymorphism and the absence of simple dinucleotide variation in 23 kb of sequence are compatible with recombination or sister chromatid exchange, but not polymerase slippage. By inference, recombination should underlie the polymorphisms at (GT)n/(AC)n since they are a subset of (RY)n and they commonly occur in the context of longer (RY)n. Which means that the introductory statement in the main article here: Recombination therefore only shuffles already existing genetic variation and does not create new variation at the involved loci. is completely incorrect. Recombination is sufficient to produce novel alleles. It does not necessarily produce novel alleles, though, which is why a misunderstanding such as the quoted statement from the article can become widespread as a meme. Can somebody fix the main article, please? --Wesley R. Elsberry 22:05, 3 January 2007 (UTC) Suggested rephrasing of the bad sentence. Was: Recombination therefore only shuffles already existing genetic variation and does not create new variation at the involved loci. should become. Because coding regions are relatively uncommon, in most cases recombination breaks and rejoins genetic material outside those regions, with the effect of "shuffling" already-existing loci. But since recombination does not respect reading frame boundaries, from time to time it will bring together parts of differing alleles, resulting in the production of a novel allele. How's that sound? --Wesley R. Elsberry 22:20, 3 January 2007 (UTC)

I emphatically disagree with Dr. Elsberry. The sentence should remain unchanged. This article is based on one of the leading cell biology textbooks in the world, co-authored by no less an authority than the late president of the National Academy of Sciences, Bruce Alberts. Note that the research article quoted by Dr. Elsberry does not say "recombination is sufficient to produce novel alleles." It simply says "By inference, recombination should underlie the polymorphisms . " Notice the use of the words "by inference" and "should." These are not words indicative of experimental certainty. I would challenge Dr. Elsberry to produce experimental evidence supporting his idea that "recombination can produce novel alleles." To my knowledge, there have been no experiments confirming this. Rather, all experimentation to date has confirmed the sentence as it stands. Therefore, to implement Dr. Elsberry's proposed change would mislead readers. Now it might be acceptable to say something like . Experiments to date indicate that recombination only shuffles already existing genetic variation and does not create new variation at the involved loci. Some evolutionary biologists have proposed that recombination can produce novel alleles by noting that recombination does not respect reading frame boundaries. However, the notion of novel allele production by recombination has not been confirmed experimentally. Readers should be aware that this change proposed by Dr. Elsberry was precipitated by a discussion on the "After the Bar Closes" Forum at Panda's Thumb. It appears that evolutionary biologists such as Dr. Elsberry are keen to propose new mechanisms for the generation of novel alleles in the face of accumulating evidence that RM + NS (Random Mutation + Natural Selection) is insufficient to explain all the biological innovations seen in nature. One participant in the discussion--a microbiology professor--even proposed that recombination is a "kind" of mutation. Of course, this would be a significant departure from all previous understandings of the word "mutation." To make the change proposed by Dr. Elsberry would be misleading to readers and in my opinion would serve to discredit the good name of Wikipedia. --David W. Hawkins 12:15, 4 January 2007 (UTC)


The most likely reason Mr. Hawkins is unaware of research demonstrating that recombination can produce new alleles is that he has not taken the time to research the subject. Allelic recombination is well represented in the scientific literature. For example from PNAS | December 10, 2002 | vol. 99 | no. 25 | 16348-16353 we have:

"Meiotic recombination in the anopheline mosquito is the major mechanism for allelic variation of PfMsp-1 (8) thus, intragenic recombination between unlike alleles generates new alleles in the progeny (10). Recombination sites are confined to the 5' and 3' regions of the gene."

Dr. Elsberry's rewrite is concise, accurate, and easy to understand, and should thus be adopted. The references from the quote are (8) Tanabe, K., Mackay, M., Goman, M. & Scaife, J. (1987) J. Mol. Biol. 195, 273-287 and (10) Kerr, P. J., Ranford-Cartwright, L. C. & Walliker, D. (1994) Mol. Biochem. Parasitol. 66, 241-248. David J. Phippard 17:14, 4 January 2007 (UTC)


In spite of Dr. Phippard's comments, the sentence, as it stands .

Recombination therefore only shuffles already existing genetic variation and does not create new variation at the involved loci.

is a correct statement. Dr. Elsberry is wrong when he states that it is completely incorrect. Note the following quotes from .

Annu. Rev. Genet. 2002. 36:75–97 doi: 10.1146/annurev.genet.36.040202.111115 Copyright c° 2002 by Annual Reviews. All rights reserved RECOMBINATION IN EVOLUTIONARY GENOMICS David Posada1,2, Keith A. Crandall3,4, and Edward C. Holmes5 1Variagenics Inc. Cambridge, Massachusetts 02139, 2Center for Cancer Research,Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, 3Department of Integrative Biology, 4Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah 84602, and 5Department of Zoology, University of Oxford,Oxford OX1 3PS, United Kingdom

Recombination can play a dominant role in the generation of novel genetic variants through the rearrangement of existing genetic variation generated through mutation." (p.81)

So while novel alleles can arise through recombination, these novel alleles are simply the rearrangement of existing genetic material which, the above authors believe, was originally created through mutation.

"Although both [homologous and non-homologous recombination] conform to a broad definition of recombination—[that is,]an evolutionary event that has as a consequence the horizontal exchange of genetic material. " (p.76)

"Horizontal exchange of genetic material" is not a phrase which gives the impression of anything truly novel being created.

Dr. Elsberry's proposed wording .

Because coding regions are relatively uncommon, in most cases recombination breaks and rejoins genetic material outside those regions, with the effect of "shuffling" already-existing loci. But since recombination does not respect reading frame boundaries, from time to time it will bring together parts of differing alleles, resulting in the production of a novel allele.

would lead readers to believe that new genetic information is being created, when in reality, previously existing information blocks are being reshuffled in a way that is not yet completely understood.

I would be interested to see what Albert's most recent textbook (2002 version) has to say about this, since this article was based on the earlier version of his textbook. I will comment on that when I can obtain a copy. --David W. Hawkins 11:05, 4 January 2007 (UTC)

Can I please say, recombination can provide mutations by accidentally duplicating alleles (a duplication event) during homologous recombination. If you want a source, look up 'homologous recombination' and 'gene duplication' on wikipedia and take the sources from there. It is well known that the third cone that contributes to human colour vision came from a duplication event. So, although recombination is not intended to produce mutations, it does on occasion. 129.67.38.36 (talk) 02:38, 8 February 2011 (UTC)

". in the first Santino junction. "

What is that? SamEV 10:42, 5 September 2006 (UTC)

Mystery solved. It was vandalism, which I've just removed. SamEV 08:09, 26 February 2007 (UTC)

The definition talks about two parents, and then about "asexually reproducing organisms" in evolutionary biology. Am I missing something? OK, it says that the initially given definition is not commonly used in certain fields (such as evolutionary biology), but it doesn't explain what definition is used in these fields. --194.145.161.227 17:34, 29 December 2006 (UTC)

David Hawkins inserted the following into the main article:

It should be noted that while a novel allele is produced in this way, no new information is being created by this process. Recombination simply rearranges existing genetic information.

This is an antievolution talking point. It comes with no substantiation whatsoever, and depends critically on leaving any coherent definition of "information" out of the discussion. While this may not meet the Wikipedia:Vandalism criteria, it comes pretty close to that. I suggest reverting to the previous version. --Wesley R. Elsberry 17:56, 5 January 2007 (UTC)

I would agree with your justification for removal. what is a novel allele if not new? Recombination rearranges existing genetic information to produce new combinations. The definition of "information" needs to be elucidated to return this statement to NPOV status. -- Serephine talk - 07:28, 9 January 2007 (UTC)

Dr. Elsberry should not be insinuating a user is a vandal on the article discussion page. He also needs to read policy on Vandalism and Dispute Resolution. I followed policy by adding to the article with well supported information (See policy below).

When someone makes an edit you consider biased or inaccurate, improve the edit, rather than reverting it. http://en.wikipedia.org/wiki/Wikipedia:Resolving_disputes

This article is now in dispute and IAW policy, I have entered a detailed but courteous dispute essay on Dr. Elsberry's Talk Page and will take up the discussion with him there until this is resolved. David W. Hawkins 02:44, 9 January 2007 (UTC)

If that was "courteous", I will take a pass on seeing what Hawkins says when he gets nasty. Since I have never edited the article, I can hardly be guilty of reverting Hawkins's edit. What I said was, "While this may not meet the Wikipedia:Vandalism criteria, it comes pretty close to that." And it does. Unable to produce a convincing case for his original point, Hawkins inserted an unsupported assertion that had nothing to do with any existing topic within the article, one that is a commonplace in the antievolution literature. When it was properly removed by JoshuaZ as an insertion of a creationist point of view, Hawkins made a false accusation about my actions. So far as following Wikipedia policy here, I have already been complying with "Step 2" from the "Resolving disputes" page I have relied upon convincing other editors of the correctness of what I say and allowing them to make, or not make, the changes that I have suggested. It was Hawkins who took direct action to insert a POV assertion without substantiation directly in the main article. --Wesley R. Elsberry 05:25, 9 January 2007 (UTC)


I see that Dr. Elsberry wants to shift responsibility for the recent changes by pointing out the users who actually implemented the changes. Fine. I will retract my accusation. However, it is Dr. Elsberry who is the driving force behind implementing these changes. I would ask Dr. Elsberry to also retract his statement that I came close to vandalism based upon the following definition .

Vandalism is any addition, deletion, or change of content made in a deliberate attempt to compromise the integrity of Wikipedia. The most common type of vandalism is the replacement of existing text with obscenities, page blanking, or the insertion of bad jokes or other nonsense. Fortunately, this kind of vandalism is usually easy to spot. Any good-faith effort to improve the encyclopedia, even if misguided or ill-considered, is not vandalism. Apparent bad-faith edits that do not make their bad-faith nature inarguably explicit are not considered vandalism at Wikipedia. For example, adding a personal opinion once is not vandalism — it's just not helpful, and should be removed or restated.

This seems to be a contentious remark especially when directed at a new user. I made a good-faith effort to improve the encyclopedia, and I am not seeking to insert my POV. From this point forward, I believe policy would dictate that we move any further discussions about rule violations to either of our user Talk Pages.

As for this article, I note that the user "Serephine" states that the definition of "information" needs to be elucidated to return my statement to NPOV status. I submit the following definition for Biological Information from Crick pointed out by Meyer .

“By information I mean the specification of the amino acid sequence in protein . . . Information means here the precise determination of sequence, either of bases in the nucleic acid or on amino acid residues in the protein” Crick, F. On Protein Synthesis. Symposium for the Society of Experimental Biology 12:138-63, esp. 144, 153, 1958. http://www.discovery.org/articleFiles/PDFs/DNAPerspectives.pdf

Thus, molecular biologists beginning with Crick equated information not only with complexity but also with “specificity,” where “specificity” or “specified” has meant “necessary to function” (Crick 1958:144, 153 Sarkar, 1996:191).3 Molecular biologists such as Monod and Crick understood biological information--the information stored in DNA and proteins--as something more than mere complexity (or improbability). Their notion of information associated both biochemical contingency and combinatorial complexity with DNA sequences (allowing DNA's carrying capacity to be calculated), but it also affirmed that sequences of nucleotides and amino acids in functioning macromolecules possessed a high degree of specificity relative to the maintenance of cellular function. http://www.discovery.org/scripts/viewDB/index.php?command=view&id=2177

In spite of Dr. Elsberry's incorrect statement that .

Which means that the introductory statement in the main article here: Recombination therefore only shuffles already existing genetic variation and does not create new variation at the involved loci. is completely incorrect.

. I do agree with his addition, not because of the reference he cited, but because of David Phippard's citation.

However, my added sentence .

It should be noted that while a novel allele is produced in this way, no new information is being created by this process. Recombination simply rearranges existing genetic information.

. is correct and helpful in understanding what is really going on. It is well supported by the Posada article, by a statement from Crick, and by further statements with references to the literature by Meyer. I will wait to hear more discussion before editing further. David W. Hawkins Afdave 12:42, 9 January 2007 (UTC)

Hawkins wrote: I see that Dr. Elsberry wants to shift responsibility Lack of courtesy noted in the promulgation of a new false accusation. I made a good-faith effort to improve the encyclopedia, and I am not seeking to insert my POV. It was because I judged Hawkins to be sincerely misguided that I originally said that his actions may not meet the criteria of Wikipedia:Vandalism. However, the insertion made by Hawkins did reduce the integrity of Wikipedia, and it was quite easily recognizable as POV insertion since it is just a common antievolution argument. From this point forward, I believe policy would dictate that we move any further discussions about rule violations to either of our user Talk Pages. Hawkins would be wrong again. Read the policy: "Either contact the other party on that user's talk page, or use the talk page associated with the article in question." This page is perfectly appropriate for handling an exchange over what should -- and should not be -- in the main article. Stephen C. Meyer is the Director of the Discovery Institute's Center for Science and Culture, a philosopher of science without experience or practice in information theory. What he offers from Crick doesn't even support Meyer's claim that biologists were incorporating functional components into their ideas about information and molecular biology it reads as a call to determine the sequence of bases or amino acids and not make assumptions about their composition in ignorance, as Meyer documents was commonplace not long before Crick's article was written. Crick was not offering a formal definition of information, but rather identifying an instance of information. The article from Meyer that Hawkins quotes was repudiated by the publisher. I suggest that it be considered inappropriate as a source of verifiable information per Wikipedia guidelines. Funny, that I should be incorrect in asserting that a statement was wrong when even Hawkins stipulates that the text that contravened it is correct. References that show that recombination does cause the formation of novel alleles trumps references that have not taken cognizance of that research. This aspect of science will continue to cause Hawkins trouble until Hawkins learns that he cannot set aside evidence by quoting people who have not yet addressed that evidence. --Wesley R. Elsberry 14:56, 9 January 2007 (UTC) Hawkins wrote: However, it is Dr. Elsberry who is the driving force behind implementing these changes. Yes, anyone who points out an error in a Wikipedia article is the driving force behind getting it changed to a more accurate state. Is there a problem in that? --Wesley R. Elsberry 15:00, 9 January 2007 (UTC)

1) Crick's statement is a very good formal definition of "biological information", which is what is being discussed here and he makes himself quite clear. However, I am not omniscient and I am willing to research the other sources that Meyer and others cite to ensure we achieve accuracy.

2) Dr. Elsberry seems to be using the fact of a later editorial committee not liking Dr. Meyer because they are anti-ID, to somehow reduce the value of the Crick statement.

3) Dr. Elsberry speaks of Dr. Meyer's lack of experience or practice in information theory, yet history is replete with examples of scientists and philosophers who crossed boundaries in varying degrees successfully. Further, is not Crick an authority?

References that show that recombination does cause the formation of novel alleles trumps references that have not taken cognizance of that research. This aspect of science will continue to cause Hawkins trouble until Hawkins learns that he cannot set aside evidence by quoting people who have not yet addressed that evidence.

Why does Dr. Elsberry imagine that Posada et. al. are not cognizant of the mentioned research? Both the Posada article and the PNAS article which admittedly support Dr. Elsberry's added language were both 2002 articles.(note that Dr. Elsberry's original citation did not support changing the article)

5) Note that Dr. Elsberry still does not understand how his early statement was incorrect. He writes .

Funny, that I should be incorrect in asserting that a statement was wrong when even Hawkins stipulates that the text that contravened it is correct.

Yes. You said that the original sentence was "completely incorrect." But this is not true. It was quite correct as the Posada article clearly shows. Had you said that it was "incomplete" or "could be expanded to include recent research" you would have been correct. But the statement you made was incorrect.

6) But that does not matter WRT the added sentences. I have accepted your added sentence and I am merely asserting that my sentence (or something very similar) should also be added

7) I will answer your last question (or further questions pertaining to rules and etiquette) on your Talk page as that seems to be more in line with Wikipedia rules where it says .

Never carry on a dispute on the article page itself.

From a comprehensive reading of the rules it does appear that pros and cons related to the article itself belong here, but that arguments over etiquette and rules should stay on the User Talk pages. David W. Hawkins Afdave 17:36, 9 January 2007 (UTC)

Meyer is not a reliable source for these purposes. He is for obvious reasons very biased and is a philosopher and theologian with no training in mathematics or biology. it is not Wikipedia's concern that "history is replete with examples of scientists and philosophers who crossed boundaries in varying degrees successfully" - if actual biologists pick up on the idea then Wikipedia could cite it. As to the Crick matter, there are a variety of defintions of information and it isn't even clear to me from the Crick quote that he wouldn't consider this to be an increase in information and concluded that it wouldn't be is thus original research. Now, if you can get a specific defintion of information and get a reliable source that specifically says that these novel allels are not adding information then we can consider including it. JoshuaZ 00:01, 16 January 2007 (UTC) Nothing else needs to be said, the above sums it up perfectly. Please, to parties involved, don't drag this out further, suck it up and do what's best in the interests of Wikipedia. It's getting tiresome and petty. -- Serephine talk - 00:14, 16 January 2007 (UTC)

As to the Crick matter, there are a variety of defintions of information and it isn't even clear to me from the Crick quote that he wouldn't consider this to be an increase in information and concluded that it wouldn't be is thus original research. Now, if you can get a specific defintion of information and get a reliable source that specifically says that these novel allels are not adding information then we can consider including it.

You say there are a variety of definitions of information, yet you don't provide any. In contrast to this, I have provided one from a quite authoritative source. And I have also provided a reliable source that says that these novel alleles simply reshuffle existing variation.

Recombination can play a dominant role in the generation of novel genetic variants through the rearrangement of existing genetic variation generated through mutation." (p.81) (From the Posada article above)

You appear to be quibbling over the exact choice of words - "variation" vs. "information". What authoritative source can you provide that refutes the clear statement from the Posada article above? How is "variation" not equivalent to "biological information" especially in light of the Crick quote?

It appears to me that Dr. Elsberry wants you to disallow my added sentence because of his own Darwinist POV. You have labeled my sentence as Creationist POV which clearly it is not. We even had another editor weigh in and say .

The definition of "information" needs to be elucidated to return this statement to NPOV status.

which I promptly did from an authoritative source. You have two authoritative sources from me which clearly establish the validity of my added sentence.

In my experience, I have found that the only ones confused about the meaning of "biological information" are those seeking to find new mechanisms for Darwinian Evolution POV in the face of accumulating evidence that previously proposed mechanisms such as Random Mutation + Natural Selection are inadequate. It appears that this might the case here with Dr. Elsberry.

A quick Google search of "biological information" turned up this 2005 article .

In order to come up with such a concise definition, we should first consider what systems biology aims to achieve, that is, the understanding of biological information, specifically the information encoded in the linear nucleotide sequence of a genome. Like written language texts, genome sequences can be represented as letters (nucleotides) and words (genes). However, understanding the lingual information of such texts requires knowledge not only of the letters and words, but also of the syntax, that is, the ordering of and relationship between the words in phrases and sentences. Likewise, understanding the biological information of genomes requires an understanding of not only the nucleotides and their arrangement into genes, but also of the syntax of biological information. http://www.nature.com/msb/journal/v1/n1/full/msb4100009.html

It seems that many practicing biologists have a very clear understanding of the meaning of "biological information" and that the notion that my statement is "Creationist POV" is itself "Darwinist POV." You have rightly asserted that Wikipedia should be impartial and not promote POV. It seems that disallowing my sentence would be a clear example of doing just that. David W. Hawkins Afdave 11:24, 19 January 2007 (UTC)

Dave said: How is "variation" not equivalent to "biological information" especially in light of the Crick quote? If it is, then you're sunk, since Posada's clear statement clearly states that rearrangement of existing genetic variation creates novel variants ie, more variation, and an increase of information. Tsumetai 17:25, 19 January 2007 (UTC)

Hmmm . interesting how you added "and an increase of information" to the Posada statement. Would you please cite where in the Posada article you found that phrase? Thanks. David W. Hawkins Afdave 10:55, 22 January 2007 (UTC)

I never presented it as an exact quote. Are you seriously going to argue that "variation" and "biological information" are equivalent, but "more variation" and "more biological information" are not? Tsumetai 14:40, 31 January 2007 (UTC)

I am arguing that it is misleading to say that "recombination . can produce novel alleles" without further explaining that these novel alleles are created from "existing genetic variation" as the Posada article makes clear.

Recombination can play a dominant role in the generation of novel genetic variants through the rearrangement of existing genetic variation generated through mutation." (p.81) "Although both [homologous and non-homologous recombination] conform to a broad definition of recombination—[that is,] an evolutionary event that has as a consequence the horizontal exchange of genetic material. " (p.76) [Posada, Reference given above]

IOW, we should not be giving readers the impression that there is new biological information (as defined by Crick) being created through this process. You could silence me on this issue by adding the following wording .

But since recombination does not respect reading frame boundaries, from time to time it will bring together parts of differing alleles, resulting in the production of a novel allele [current wording] through the rearrangement of existing genetic variation. [added] [Straight from the Posada article]

This way we don't get into the debate over the definitions of "biological information", yet we don't mislead our readers by implying that new biological information is being created through this process.

Is that a fair compromise? JoshuaZ, can you please implement this change? Thx. 71.1.124.104 11:34, 12 February 2007 (UTC)Afdave

That clarification might be redundant, but the opening paragraph is a bit clunky and that little bit of "increased information" might be helpful. I've made the change. Dphippard 23:44, 13 February 2007 (UTC)

"This way we don't get into the debate over the definitions of "biological information", yet we don't mislead our readers by implying that new biological information is being created through this process."

It would be misleading to readers to pretend that a novel allele, however it comes into existence, is anything other than new biological information. The objection that a novel allele made by rearranging existing genetic information cannot be considered new biological information is parallel to the objection that a book comprised of words found in a dictionary cannot be considered a new literary work. --Wesley R. Elsberry 10:37, 20 February 2007 (UTC)

I like analogies also. But I believe Dr. Elsberry's analogy is flawed. His book analogy implies that recombination is responsible for the origination (innovation) of form in addition to the diversification (variation) of form. Muller and Newman address this thoroughly .

Origination of Organismal Form: The Forgotten Cause in Evolutionary Theory Gerd B. Müller and Stuart A. Newman http://mitpress.mit.edu/books/chapters/0262134195chap1.pdf (Cited in Meyer's "Smithsonian" paper found here http://www.discovery.org/scripts/viewDB/index.php?command=view&id=2177) pp. 1-2 Evolutionary biology arose from the age-old desire to understand the origin and the diversification of organismal forms. During the past 150 years, the question of how these two aspects of evolution are causally realized has become a field of scientific inquiry, and the standard answer, encapsulated in a central tenet of Darwinism, is by “variation of traits” and “natural selection.” The modern version of this tenet holds that the continued modification and inheritance of a basic genetic tool kit for the regulation of developmental processes, directed by mechanisms acting at the population level, has generated the panoply of organismal body plans encountered in nature. This notion is superimposed on a sophisticated, mathematically based population genetics, which became the dominant mode of evolutionary biology in the second half of the twentieth century. As a consequence, much of present-day evolutionary theory is concerned with formal accounts of quantitative variation and diversification. Other major branches of evolutionary biology have concentrated on patterns of evolution, ecological factors, and, increasingly, on the associated molecular changes. Indeed, the concern with the “gene” has overwhelmed all other aspects, and evolutionary biology today has become almost synonymous with evolutionary genetics. These developments have edged the field farther and farther away from the second initial theme: the origin of organismal form and structure. The question of why and how certain forms appear in organismal evolution addresses not what is being maintained (and quantitatively varied) but rather what is being generated in a qualitative sense. This causal question concerning the specific generative mechanisms that underlie the origin and innovation of phenotypic characters is probably best embodied in the term origination, which will be used in this sense throughout this volume. That this causal question has largely disappeared from evolutionary biology is partly hidden by the semantics of modern genetics, which purports to provide answers to the question of causation, but these answers turn out to be largely restricted to the proximate causes of local form generation in individual development. The molecular mechanisms that bring about biological form in modern-day embryos, however, should not be confused with the causes that led to the appearance of these forms in the first place. Although the forces driving morphological evolution certainly include natural selection, the appearance of specific, phenotypic elements of construction must not be taken as being caused by natural selection selection can only work on what already exists. Darwin acknowledges this point in the first edition of The Origin of Species, where he states that certain characters may have “originated from quite secondary causes, independently from natural selection” (Darwin, 1859, 196), although he attributes “little importance” to such effects. In a modified version of the same paragraph in the sixth edition (Darwin, 1872, 157), he concedes that “we may easily err in attributing importance to characters, and in believing that they have been developed through natural selection.” It is the aim of the present volume to elaborate on this distinction between the origination (innovation) and the diversification (variation) of form by focusing on the plurality of causal factors responsible for the former, relatively neglected aspect, the origination of organismal form. Failure to incorporate this aspect represents one of the major gaps in the canonical theory of evolution, it being quite distinct from the topics with which population genetics or developmental genetics is primarily concerned. As a starting point, we will briefly outline the central questions that arise in the context of origination.

I think the book/dictionary analogy would be good if we compared, for example, Homer's Iliad to the human genome and Gone With the Wind to the horse genome, to pick some higher organisms. I will allow the geneticists here to correct me if I am wrong, but my understanding is that genetic recombination would be analogous to writing a new book using only the existing words in a particular book, such as one of the examples above, NOT the whole dictionary. Yes, the reading frame boundaries are not always respected, implying an analogy of selecting the new word 'HERE' from the previously existing words 'tHE REal story', for example. But this is quite a different analogy from the one given by Dr. Elsberry. Nature does not select a subset of the 'words' in the 'dictionary' to create biological innovation, as Dr. Elsberry's analogy implies. Nature selects ALL the existing 'words' and 'letters' of the genome, recombines them under tight cellular control and produces a new organism displaying relatively minor differences from the previously existing organism. Nothing resembling the creation of biological innovation has ever been demonstrated by recombination. David W. Hawkins Afdave 15:57, 13 March 2007 (UTC)

Muller and Newman don't address the role of recombination as a source of novel alleles. "Recombination" does not even appear in the linked PDF. Muller and Newman argue for non-genetic components and processes as being the locus of most evolutionary innovation they do not argue for exclusive generative ability being due to those components and processes. The linked text is very much high-level and their references to actual research are few in number. The linked article does not in any case set aside the research cited by Phippard, which Hawkins has already stipulated does establish the ability of recombination to produce novel alleles. Novel alleles are new biological information, contrary to Hawkins's idee fixe and title of this subsection. Certainly the fact of citation of Muller and Newman by Meyer adds nothing to the discussion. Nor did I offer the literary scenario as an analogy for the genetics. Please read more carefully in the future. --13:35, 15 March 2007 (UTC)

Hmmm . I did read you very carefully (Dr. Elsberry I assume?) and it appears that you did indeed offer the literary scenario as an analogy for the genetics. You wrote .

The objection that a novel allele made by rearranging existing genetic information cannot be considered new biological information is parallel to the objection that a book comprised of words found in a dictionary cannot be considered a new literary work. --Wesley R. Elsberry

It would therefore appear that my analysis of your analogy is accurate. Afdave 14:57, 26 April 2007 (UTC)

A question for both sides of the dispute: how to name this example: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1180228/ ? Could creation of a fusion gene in the process of recombination count as creation of a novel allele? The above example seems to support Dr. Elsberry's position. 80.240.162.190 (talk) 03:36, 16 January 2013 (UTC)

If anyone has an argument against this, please say something. In fact, I notice now that the argument has been made before now, but no merge tag had been placed on the article. -Madeleine 01:20, 29 March 2007 (UTC)

  • Add to each of sections for other types of recombination the same "Main article: Foo" note at the top. should point here rather than to chromosomal crossover, and there should be information on homologous vs. nonhomologous recombination here. I have to think about how to actually summarize the topic on this page, but the redirect to chromosomal crossover contributed to my initial suggestion to merge.
  • The category levels of "crossing over" vs. "other types of recombination" needs to be reconsidered. Perhaps all types of recombination should be categories on the same level. Alternatively, it could be "homologous" vs "nonhomologous" recombination, with the different types of recombination within each, but since site-specific recombination uses "partial" homology this is might just be confusing to the reader.
  • As Peta suggested, information specific to chromosomal crossover should be moved to the crossover page such that chromosomal crossover does not dominate the information content of this article.

In evolutionary biology this shuffling of genes is thought to have many advantages, including that of allowing sexually reproducing organisms to avoid Muller's ratchet.

should say asexually instread of sexually.

I think perhaps you are misreading it, it looks correct to me. Madeleine ✉ ✍ 13:35, 14 April 2008 (UTC)

This extra 'a' has caused me so much trouble. It should in fact be 'sexually', pointing out that asexual organisms must deal with Muller's Ratchet. If you think about it, recombination between two chromosomes in an asexual organism would merely pass a mutated allele from one chromosome to another, it would not deal with it. If only I'd thought about that before I spent about an hour trawling through wikipedia and the internet trying to discover if asexual organisms undergo recombination. 129.67.38.36 (talk) 02:48, 8 February 2011 (UTC)

Maybe the confusion arises because recombination occurs both in non-sexual context and (the vast majority) in systems that mate. Maybe recombination is here intended to refer to non-sexual recombination, as for example in bacteria. I.e. Even though asexual organisms should be prone to amass negatively affecting mutations, some types can escape by the application of exotic kinds of recombination, for example bacterial conjugation. --Ettrig (talk) 05:51, 8 February 2011 (UTC)

The definition of recombination used in the article - the breaking and rejoining of DNA strands to form new molecules of DNA - must be wrong. Doesn't recombination includes, in addition to croosing over and the other mechanisms cited in the article, the pairing of homologous chromosomes (and the independent assortment)[1]? By the definition in Griffiths' Introduction to Genetic Analysis, chapter 3, recombination is production of new combinations of aleles (which is made by homologous pairing, too).

  • "Recombination (Bridges & Morgan 1923) — any process which gives rise to cells or individuals (recombinants) associating in new ways two or more hereditary determinants (genes) by which their parents differed (⇒ genetic recombination)."
  • "Genetic recombination — in a broad sense, any process by means of which two (or more) "parents" (organisms, cells, or molecules containing ⇒ genetic information) with different genetic characters pair, interact, and give rise to progeny (recombinant individuals, cells, or molecules) so that genes in which the parents differed are associated in new combinations (e.g., from AB and ab the recombinants Ab and aB are produced). The molecular mechanism of g. r. is not yet understood. The products of g. r. (the recombinants) may be detected after meiosis (meiotic recombination), after mitosis (in the case of mitotic recombination) or after equivalent processes occurring in bacteria and during multiplication of viruses. . " (there follows a very long discussion of different mechanisms).
  • "Assortment — in ⇒ meiosis, the normally random, in certain cases, non-random ("preferential") distribution to the cell poles of whole chromosomes (during Anaphase I) contained in pairing configurations (⇒ chromosome pairing) and of chromatids (during anaphase II) resulting in random or non-random ⇒ segregation and ⇒ genetic recombination of genes." (then two subsections, one on "Random or independent assortment" and one on "Non-random assortment".

I like that this article has attracted more attention over the past several months. Genetic recombination is process of fundamental importance in biology and deserves a brilliant article. Below are a few comments and suggestions.

The current lead seems like it could be improved with regard to accessibility and summary style. I'm a bit biased, but I think a version of the lead from a few years ago fares better in these areas. What are others' thoughts on reverting back to that older version?

Also, when I look at this article and Homologous recombination, I see a high degree of redundancy. For example, compare the diagram in Genetic_recombination#Meiotic_recombination to the second diagram in Homologous_recombination#In_eukaryotes. This article's discussion of crossover and non-crossover products and their relation to the DHJ / DSBR and SDSA pathways is also covered in Homologous_recombination#Models. Genetic_recombination#Recombinational_repair is variously covered in Homologous_recombination#Effects_of_dysfunction, Homologous_recombination#Cancer_therapy and Homologous_recombination#In_viruses.

Some redundancy between this article and the one on homologous recombination would not necessarily be a bad thing. What I think is worth avoiding though is conflating how we discuss the two subjects. Genetic recombination is a broad class of biological process that includes:

Differentiating between these terms could help improve the article's accessibility. I think the article currently dives into too much depth about, for example, the DHJ and SDSA pathways of recombination in meiosis. The homologous recombination article is better suited for that degree of detail. Even then, the degree of detail might be excessive -- that was a chief critique in Wikipedia:Featured_article_candidates/Homologous_recombination/archive1. I think it would be best for this article to summarize those articles in several paragraphs each, and let those articles discuss their respective topics in greater detail.

This article should be much higher level and more accessible. In my opinion, genetic recombination should be aimed at high school students studying biology and lower-level undergraduates, homologous recombination and V(D)J recombination should be aimed at undergraduates majoring in the biological sciences, and articles about specific biochemical pathways of recombination like RecF pathway should be aimed at upper-level undergraduates, graduate students, and researchers. Emw (talk) 01:51, 25 October 2013 (UTC)

I agree that genetic recombination is a process of fundamental importance. The version of the lead from a few years ago stated "Genetic recombination is a process by which a molecule of nucleic acid (usually DNA but can also be RNA) is broken and then joined to a different DNA molecule. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules of DNA as in non-homologous end joining. Recombination is a common method of DNA repair in both bacteria and eukaryotes. In eukaryotes, recombination also occurs in meiosis where it facilitates chromosomal crossover. The crossover process leads to offspring having different combinations of genes from their parents, and can occasionally produce new chimeric alleles. In organisms with an adaptive immune system, a type of genetic recombination called V(D)J recombination helps immune cells rapidly diversify and adapt to recognize new pathogens. The shuffling of genes brought about by genetic recombination is thought to have many advantages, as it is a major engine of genetic variation and also allows asexually reproducing organisms to avoid Muller's ratchet, in which the genomes of an asexual population accumulate deleterious mutations in an irreversible manner." However the previous lead indicated that genetic recombination only resulted from breakage and exchange. Evidence over the last decade indicates that SDSA, which does not involve breakage and exchange, but rather information exchange, is a more more common type of recombination in meiosis, and SDSA is even more common during mitosis. The previous lead also indicated that non-homologous end joining is recombination between dissimilar molecules of DNA. Actually, non-homologous end joining is a form of inaccurate repair that leads to mutations, but is not ordinarily regarded as a form of genetic recombination since it merely rejoins broken ends. The previous lead said "The shuffling of genes brought about by genetic recombination is thought to have many advantages, as it is a major engine of genetic variation." However, the specific advantages conferred by genetic variation is a highly controversial area of genetics. The referral to "many advantages" is an over-enthusiastic characterization of current thinking, since there is very little agreement among authorities in the field. For these reasons, among others, I think the current lead is preferable. I agree that some redundancy between this article and the one on homologous recombination would not necessarily be a bad thing. To make the articles less redundant of each other, it would be helpful to considerably expand the discussion of V(D)J recombination, important in immunology, and expand the discussion of site specific recombination, important in lysogeny of bacteriophage, mating type switching in yeast, genetic engineering and pathogenic phase variation as a method for dealing with rapidly varying environments without requiring random mutation (employed by various types of bacteria, including Salmonella species). However, this is too much for me to undertake at this time. I think this article needs to reflect current knowledge and understanding in the field of genetic recombination. Thus, I believe it needs the details given to allow understanding of the current state of knowledge.Bernstein0275 (talk) 00:43, 30 October 2013 (UTC)

The comment(s) below were originally left at Talk:Genetic recombination/Comments , and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated if so, please feel free to remove this section.

rated top as high school/SAT biology content - tameeria 15:05, 17 February 2007 (UTC) The article needs a clearer definition/distinction between meiotic recombination (chromosome crossover) and other types of naturally occuring genetic recombination, e.g. in prokaryotes or in immune cells, yeast mating type determination etc. - tameeria 18:14, 18 February 2007 (UTC)

Last edited at 18:14, 18 February 2007 (UTC). Substituted at 15:55, 29 April 2016 (UTC)

Unfortunately, this article is not accessible to a lay audience. It would be a grand thing if someone who understands this material would completely rewrite the article in an accessible way. Strebe (talk) 16:58, 21 April 2018 (UTC)


Contents

DNA damage, due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 10,000 to 1,000,000 molecular lesions per cell per day. [2] While this constitutes only 0.000165% of the human genome's approximately 6 billion bases, unrepaired lesions in critical genes (such as tumor suppressor genes) can impede a cell's ability to carry out its function and appreciably increase the likelihood of tumor formation and contribute to tumour heterogeneity.

The vast majority of DNA damage affects the primary structure of the double helix that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules' regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable to the effects of DNA damage.

Sources Edit

DNA damage can be subdivided into two main types:

    damage such as attack by reactive oxygen species produced from normal metabolic byproducts (spontaneous mutation), especially the process of oxidative deamination
    1. also includes replication errors
    1. ultraviolet [UV 200–400 nm] radiation from the sun or other artificial light sources
    2. other radiation frequencies, including x-rays and gamma rays or thermal disruption
    3. certain planttoxins
    4. human-made mutagenic chemicals, especially aromatic compounds that act as DNA intercalating agents[8]

    The replication of damaged DNA before cell division can lead to the incorporation of wrong bases opposite damaged ones. Daughter cells that inherit these wrong bases carry mutations from which the original DNA sequence is unrecoverable (except in the rare case of a back mutation, for example, through gene conversion).

    Types Edit

    There are several types of damage to DNA due to endogenous cellular processes:

    1. oxidation of bases [e.g. 8-oxo-7,8-dihydroguanine (8-oxoG)] and generation of DNA strand interruptions from reactive oxygen species,
    2. alkylation of bases (usually methylation), such as formation of 7-methylguanosine, 1-methyladenine, 6-O-Methylguanine
    3. hydrolysis of bases, such as deamination, depurination, and depyrimidination. (e.g., benzo[a]pyrene diol epoxide-dG adduct, aristolactam I-dA adduct)
    4. mismatch of bases, due to errors in DNA replication, in which the wrong DNA base is stitched into place in a newly forming DNA strand, or a DNA base is skipped over or mistakenly inserted.
    5. Monoadduct damage cause by change in single nitrogenous base of DNA
    6. Diadduct damage

    Damage caused by exogenous agents comes in many forms. Some examples are:

    1. UV-B light causes crosslinking between adjacent cytosine and thymine bases creating pyrimidine dimers. This is called direct DNA damage.
    2. UV-A light creates mostly free radicals. The damage caused by free radicals is called indirect DNA damage.
    3. Ionizing radiation such as that created by radioactive decay or in cosmic rays causes breaks in DNA strands. Intermediate-level ionizing radiation may induce irreparable DNA damage (leading to replicational and transcriptional errors needed for neoplasia or may trigger viral interactions) leading to pre-mature aging and cancer.
    4. Thermal disruption at elevated temperature increases the rate of depurination (loss of purine bases from the DNA backbone) and single-strand breaks. For example, hydrolytic depurination is seen in the thermophilic bacteria, which grow in hot springs at 40–80 °C. [9][10] The rate of depurination (300 purine residues per genome per generation) is too high in these species to be repaired by normal repair machinery, hence a possibility of an adaptive response cannot be ruled out.
    5. Industrial chemicals such as vinyl chloride and hydrogen peroxide, and environmental chemicals such as polycyclic aromatic hydrocarbons found in smoke, soot and tar create a huge diversity of DNA adducts- ethenobases, oxidized bases, alkylated phosphotriesters and crosslinking of DNA, just to name a few.

    UV damage, alkylation/methylation, X-ray damage and oxidative damage are examples of induced damage. Spontaneous damage can include the loss of a base, deamination, sugar ring puckering and tautomeric shift. Constitutive (spontaneous) DNA damage caused by endogenous oxidants can be detected as a low level of histone H2AX phosphorylation in untreated cells. [11]

    Nuclear versus mitochondrial Edit

    In human cells, and eukaryotic cells in general, DNA is found in two cellular locations – inside the nucleus and inside the mitochondria. Nuclear DNA (nDNA) exists as chromatin during non-replicative stages of the cell cycle and is condensed into aggregate structures known as chromosomes during cell division. In either state the DNA is highly compacted and wound up around bead-like proteins called histones. Whenever a cell needs to express the genetic information encoded in its nDNA the required chromosomal region is unravelled, genes located therein are expressed, and then the region is condensed back to its resting conformation. Mitochondrial DNA (mtDNA) is located inside mitochondria organelles, exists in multiple copies, and is also tightly associated with a number of proteins to form a complex known as the nucleoid. Inside mitochondria, reactive oxygen species (ROS), or free radicals, byproducts of the constant production of adenosine triphosphate (ATP) via oxidative phosphorylation, create a highly oxidative environment that is known to damage mtDNA. A critical enzyme in counteracting the toxicity of these species is superoxide dismutase, which is present in both the mitochondria and cytoplasm of eukaryotic cells.

    Senescence and apoptosis Edit

    Senescence, an irreversible process in which the cell no longer divides, is a protective response to the shortening of the chromosome ends. The telomeres are long regions of repetitive noncoding DNA that cap chromosomes and undergo partial degradation each time a cell undergoes division (see Hayflick limit). [12] In contrast, quiescence is a reversible state of cellular dormancy that is unrelated to genome damage (see cell cycle). Senescence in cells may serve as a functional alternative to apoptosis in cases where the physical presence of a cell for spatial reasons is required by the organism, [13] which serves as a "last resort" mechanism to prevent a cell with damaged DNA from replicating inappropriately in the absence of pro-growth cellular signaling. Unregulated cell division can lead to the formation of a tumor (see cancer), which is potentially lethal to an organism. Therefore, the induction of senescence and apoptosis is considered to be part of a strategy of protection against cancer. [14]

    Mutation Edit

    It is important to distinguish between DNA damage and mutation, the two major types of error in DNA. DNA damage and mutation are fundamentally different. Damage results in physical abnormalities in the DNA, such as single- and double-strand breaks, 8-hydroxydeoxyguanosine residues, and polycyclic aromatic hydrocarbon adducts. DNA damage can be recognized by enzymes, and thus can be correctly repaired if redundant information, such as the undamaged sequence in the complementary DNA strand or in a homologous chromosome, is available for copying. If a cell retains DNA damage, transcription of a gene can be prevented, and thus translation into a protein will also be blocked. Replication may also be blocked or the cell may die.

    In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation cannot be repaired. At the cellular level, mutations can cause alterations in protein function and regulation. Mutations are replicated when the cell replicates. In a population of cells, mutant cells will increase or decrease in frequency according to the effects of the mutation on the ability of the cell to survive and reproduce.

    Although distinctly different from each other, DNA damage and mutation are related because DNA damage often causes errors of DNA synthesis during replication or repair these errors are a major source of mutation.

    Given these properties of DNA damage and mutation, it can be seen that DNA damage is a special problem in non-dividing or slowly-dividing cells, where unrepaired damage will tend to accumulate over time. On the other hand, in rapidly-dividing cells, unrepaired DNA damage that does not kill the cell by blocking replication will tend to cause replication errors and thus mutation. The great majority of mutations that are not neutral in their effect are deleterious to a cell's survival. Thus, in a population of cells composing a tissue with replicating cells, mutant cells will tend to be lost. However, infrequent mutations that provide a survival advantage will tend to clonally expand at the expense of neighboring cells in the tissue. This advantage to the cell is disadvantageous to the whole organism, because such mutant cells can give rise to cancer. Thus, DNA damage in frequently dividing cells, because it gives rise to mutations, is a prominent cause of cancer. In contrast, DNA damage in infrequently-dividing cells is likely a prominent cause of aging. [15]

    Cells cannot function if DNA damage corrupts the integrity and accessibility of essential information in the genome (but cells remain superficially functional when non-essential genes are missing or damaged). Depending on the type of damage inflicted on the DNA's double helical structure, a variety of repair strategies have evolved to restore lost information. If possible, cells use the unmodified complementary strand of the DNA or the sister chromatid as a template to recover the original information. Without access to a template, cells use an error-prone recovery mechanism known as translesion synthesis as a last resort.

    Damage to DNA alters the spatial configuration of the helix, and such alterations can be detected by the cell. Once damage is localized, specific DNA repair molecules bind at or near the site of damage, inducing other molecules to bind and form a complex that enables the actual repair to take place.

    Direct reversal Edit

    Cells are known to eliminate three types of damage to their DNA by chemically reversing it. These mechanisms do not require a template, since the types of damage they counteract can occur in only one of the four bases. Such direct reversal mechanisms are specific to the type of damage incurred and do not involve breakage of the phosphodiester backbone. The formation of pyrimidine dimers upon irradiation with UV light results in an abnormal covalent bond between adjacent pyrimidine bases. The photoreactivation process directly reverses this damage by the action of the enzyme photolyase, whose activation is obligately dependent on energy absorbed from blue/UV light (300–500 nm wavelength) to promote catalysis. [16] Photolyase, an old enzyme present in bacteria, fungi, and most animals no longer functions in humans, [17] who instead use nucleotide excision repair to repair damage from UV irradiation. Another type of damage, methylation of guanine bases, is directly reversed by the protein methyl guanine methyl transferase (MGMT), the bacterial equivalent of which is called ogt. This is an expensive process because each MGMT molecule can be used only once that is, the reaction is stoichiometric rather than catalytic. [18] A generalized response to methylating agents in bacteria is known as the adaptive response and confers a level of resistance to alkylating agents upon sustained exposure by upregulation of alkylation repair enzymes. [19] The third type of DNA damage reversed by cells is certain methylation of the bases cytosine and adenine.

    Single-strand damage Edit

    When only one of the two strands of a double helix has a defect, the other strand can be used as a template to guide the correction of the damaged strand. In order to repair damage to one of the two paired molecules of DNA, there exist a number of excision repair mechanisms that remove the damaged nucleotide and replace it with an undamaged nucleotide complementary to that found in the undamaged DNA strand. [18]

      (BER): damaged single bases or nucleotides are most commonly repaired by removing the base or the nucleotide involved and then inserting the correct base or nucleotide. In base excision repair, a glycosylase[20] enzyme removes the damaged base from the DNA by cleaving the bond between the base and the deoxyribose. These enzymes remove a single base to create an apurinic or apyrimidinic site (AP site). [20] Enzymes called AP endonucleasesnick the damaged DNA backbone at the AP site. DNA polymerase then removes the damaged region using its 5’ to 3’ exonuclease activity and correctly synthesizes the new strand using the complementary strand as a template. [20] The gap is then sealed by enzyme DNA ligase. [21] (NER): bulky, helix-distorting damage, such as pyrimidine dimerization caused by UV light is usually repaired by a three-step process. First the damage is recognized, then 12-24 nucleotide-long strands of DNA are removed both upstream and downstream of the damage site by endonucleases, and the removed DNA region is then resynthesized. [22] NER is a highly evolutionarily conserved repair mechanism and is used in nearly all eukaryotic and prokaryotic cells. [22] In prokaryotes, NER is mediated by Uvr proteins. [22] In eukaryotes, many more proteins are involved, although the general strategy is the same. [22] systems are present in essentially all cells to correct errors that are not corrected by proofreading. These systems consist of at least two proteins. One detects the mismatch, and the other recruits an endonuclease that cleaves the newly synthesized DNA strand close to the region of damage. In E. coli , the proteins involved are the Mut class proteins: MutS, MutL, and MutH. In most Eukaryotes, the analog for MutS is MSH and the analog for MutL is MLH. MutH is only present in bacteria. This is followed by removal of damaged region by an exonuclease, resynthesis by DNA polymerase, and nick sealing by DNA ligase. [23]

    Double-strand breaks Edit

    Double-strand breaks, in which both strands in the double helix are severed, are particularly hazardous to the cell because they can lead to genome rearrangements. In fact, when a double-strand break is accompanied by a cross-linkage joining the two strands at the same point, neither strand can be used as a template for the repair mechanisms, so that the cell will not be able to complete mitosis when it next divides, and will either die or, in rare cases, undergo a mutation. [3] [4] Three mechanisms exist to repair double-strand breaks (DSBs): non-homologous end joining (NHEJ), microhomology-mediated end joining (MMEJ), and homologous recombination (HR). [18] [24] In an in vitro system, MMEJ occurred in mammalian cells at the levels of 10–20% of HR when both HR and NHEJ mechanisms were also available. [25]

    In NHEJ, DNA Ligase IV, a specialized DNA ligase that forms a complex with the cofactor XRCC4, directly joins the two ends. [26] To guide accurate repair, NHEJ relies on short homologous sequences called microhomologies present on the single-stranded tails of the DNA ends to be joined. If these overhangs are compatible, repair is usually accurate. [27] [28] [29] [30] NHEJ can also introduce mutations during repair. Loss of damaged nucleotides at the break site can lead to deletions, and joining of nonmatching termini forms insertions or translocations. NHEJ is especially important before the cell has replicated its DNA, since there is no template available for repair by homologous recombination. There are "backup" NHEJ pathways in higher eukaryotes. [31] Besides its role as a genome caretaker, NHEJ is required for joining hairpin-capped double-strand breaks induced during V(D)J recombination, the process that generates diversity in B-cell and T-cell receptors in the vertebrate immune system. [32]

    Homologous recombination requires the presence of an identical or nearly identical sequence to be used as a template for repair of the break. The enzymatic machinery responsible for this repair process is nearly identical to the machinery responsible for chromosomal crossover during meiosis. This pathway allows a damaged chromosome to be repaired using a sister chromatid (available in G2 after DNA replication) or a homologous chromosome as a template. DSBs caused by the replication machinery attempting to synthesize across a single-strand break or unrepaired lesion cause collapse of the replication fork and are typically repaired by recombination.

    MMEJ starts with short-range end resection by MRE11 nuclease on either side of a double-strand break to reveal microhomology regions. [25] In further steps, [33] Poly (ADP-ribose) polymerase 1 (PARP1) is required and may be an early step in MMEJ. There is pairing of microhomology regions followed by recruitment of flap structure-specific endonuclease 1 (FEN1) to remove overhanging flaps. This is followed by recruitment of XRCC1–LIG3 to the site for ligating the DNA ends, leading to an intact DNA. MMEJ is always accompanied by a deletion, so that MMEJ is a mutagenic pathway for DNA repair. [34]

    The extremophile Deinococcus radiodurans has a remarkable ability to survive DNA damage from ionizing radiation and other sources. At least two copies of the genome, with random DNA breaks, can form DNA fragments through annealing. Partially overlapping fragments are then used for synthesis of homologous regions through a moving D-loop that can continue extension until they find complementary partner strands. In the final step there is crossover by means of RecA-dependent homologous recombination. [35]

    Topoisomerases introduce both single- and double-strand breaks in the course of changing the DNA's state of supercoiling, which is especially common in regions near an open replication fork. Such breaks are not considered DNA damage because they are a natural intermediate in the topoisomerase biochemical mechanism and are immediately repaired by the enzymes that created them.

    Translesion synthesis Edit

    Translesion synthesis (TLS) is a DNA damage tolerance process that allows the DNA replication machinery to replicate past DNA lesions such as thymine dimers or AP sites. [36] It involves switching out regular DNA polymerases for specialized translesion polymerases (i.e. DNA polymerase IV or V, from the Y Polymerase family), often with larger active sites that can facilitate the insertion of bases opposite damaged nucleotides. The polymerase switching is thought to be mediated by, among other factors, the post-translational modification of the replication processivity factor PCNA. Translesion synthesis polymerases often have low fidelity (high propensity to insert wrong bases) on undamaged templates relative to regular polymerases. However, many are extremely efficient at inserting correct bases opposite specific types of damage. For example, Pol η mediates error-free bypass of lesions induced by UV irradiation, whereas Pol ι introduces mutations at these sites. Pol η is known to add the first adenine across the T^T photodimer using Watson-Crick base pairing and the second adenine will be added in its syn conformation using Hoogsteen base pairing. From a cellular perspective, risking the introduction of point mutations during translesion synthesis may be preferable to resorting to more drastic mechanisms of DNA repair, which may cause gross chromosomal aberrations or cell death. In short, the process involves specialized polymerases either bypassing or repairing lesions at locations of stalled DNA replication. For example, Human DNA polymerase eta can bypass complex DNA lesions like guanine-thymine intra-strand crosslink, G[8,5-Me]T, although it can cause targeted and semi-targeted mutations. [37] Paromita Raychaudhury and Ashis Basu [38] studied the toxicity and mutagenesis of the same lesion in Escherichia coli by replicating a G[8,5-Me]T-modified plasmid in E. coli with specific DNA polymerase knockouts. Viability was very low in a strain lacking pol II, pol IV, and pol V, the three SOS-inducible DNA polymerases, indicating that translesion synthesis is conducted primarily by these specialized DNA polymerases. A bypass platform is provided to these polymerases by Proliferating cell nuclear antigen (PCNA). Under normal circumstances, PCNA bound to polymerases replicates the DNA. At a site of lesion, PCNA is ubiquitinated, or modified, by the RAD6/RAD18 proteins to provide a platform for the specialized polymerases to bypass the lesion and resume DNA replication. [39] [40] After translesion synthesis, extension is required. This extension can be carried out by a replicative polymerase if the TLS is error-free, as in the case of Pol η, yet if TLS results in a mismatch, a specialized polymerase is needed to extend it Pol ζ. Pol ζ is unique in that it can extend terminal mismatches, whereas more processive polymerases cannot. So when a lesion is encountered, the replication fork will stall, PCNA will switch from a processive polymerase to a TLS polymerase such as Pol ι to fix the lesion, then PCNA may switch to Pol ζ to extend the mismatch, and last PCNA will switch to the processive polymerase to continue replication.

    Cells exposed to ionizing radiation, ultraviolet light or chemicals are prone to acquire multiple sites of bulky DNA lesions and double-strand breaks. Moreover, DNA damaging agents can damage other biomolecules such as proteins, carbohydrates, lipids, and RNA. The accumulation of damage, to be specific, double-strand breaks or adducts stalling the replication forks, are among known stimulation signals for a global response to DNA damage. [41] The global response to damage is an act directed toward the cells' own preservation and triggers multiple pathways of macromolecular repair, lesion bypass, tolerance, or apoptosis. The common features of global response are induction of multiple genes, cell cycle arrest, and inhibition of cell division.

    Initial steps Edit

    The packaging of eukaryotic DNA into chromatin presents a barrier to all DNA-based processes that require recruitment of enzymes to their sites of action. To allow DNA repair, the chromatin must be remodeled. In eukaryotes, ATP dependent chromatin remodeling complexes and histone-modifying enzymes are two predominant factors employed to accomplish this remodeling process. [42]

    Chromatin relaxation occurs rapidly at the site of a DNA damage. [43] [44] In one of the earliest steps, the stress-activated protein kinase, c-Jun N-terminal kinase (JNK), phosphorylates SIRT6 on serine 10 in response to double-strand breaks or other DNA damage. [45] This post-translational modification facilitates the mobilization of SIRT6 to DNA damage sites, and is required for efficient recruitment of poly (ADP-ribose) polymerase 1 (PARP1) to DNA break sites and for efficient repair of DSBs. [45] PARP1 protein starts to appear at DNA damage sites in less than a second, with half maximum accumulation within 1.6 seconds after the damage occurs. [46] PARP1 synthesizes polymeric adenosine diphosphate ribose (poly (ADP-ribose) or PAR) chains on itself. Next the chromatin remodeler ALC1 quickly attaches to the product of PARP1 action, a poly-ADP ribose chain, and ALC1 completes arrival at the DNA damage within 10 seconds of the occurrence of the damage. [44] About half of the maximum chromatin relaxation, presumably due to action of ALC1, occurs by 10 seconds. [44] This then allows recruitment of the DNA repair enzyme MRE11, to initiate DNA repair, within 13 seconds. [46]

    γH2AX, the phosphorylated form of H2AX is also involved in the early steps leading to chromatin decondensation after DNA double-strand breaks. The histone variant H2AX constitutes about 10% of the H2A histones in human chromatin. [47] γH2AX (H2AX phosphorylated on serine 139) can be detected as soon as 20 seconds after irradiation of cells (with DNA double-strand break formation), and half maximum accumulation of γH2AX occurs in one minute. [47] The extent of chromatin with phosphorylated γH2AX is about two million base pairs at the site of a DNA double-strand break. [47] γH2AX does not, itself, cause chromatin decondensation, but within 30 seconds of irradiation, RNF8 protein can be detected in association with γH2AX. [48] RNF8 mediates extensive chromatin decondensation, through its subsequent interaction with CHD4, [49] a component of the nucleosome remodeling and deacetylase complex NuRD.

    DDB2 occurs in a heterodimeric complex with DDB1. This complex further complexes with the ubiquitin ligase protein CUL4A [50] and with PARP1. [51] This larger complex rapidly associates with UV-induced damage within chromatin, with half-maximum association completed in 40 seconds. [50] The PARP1 protein, attached to both DDB1 and DDB2, then PARylates (creates a poly-ADP ribose chain) on DDB2 that attracts the DNA remodeling protein ALC1. [51] Action of ALC1 relaxes the chromatin at the site of UV damage to DNA. This relaxation allows other proteins in the nucleotide excision repair pathway to enter the chromatin and repair UV-induced cyclobutane pyrimidine dimer damages.

    After rapid chromatin remodeling, cell cycle checkpoints are activated to allow DNA repair to occur before the cell cycle progresses. First, two kinases, ATM and ATR are activated within 5 or 6 minutes after DNA is damaged. This is followed by phosphorylation of the cell cycle checkpoint protein Chk1, initiating its function, about 10 minutes after DNA is damaged. [52]

    DNA damage checkpoints Edit

    After DNA damage, cell cycle checkpoints are activated. Checkpoint activation pauses the cell cycle and gives the cell time to repair the damage before continuing to divide. DNA damage checkpoints occur at the G1/S and G2/M boundaries. An intra-S checkpoint also exists. Checkpoint activation is controlled by two master kinases, ATM and ATR. ATM responds to DNA double-strand breaks and disruptions in chromatin structure, [53] whereas ATR primarily responds to stalled replication forks. These kinases phosphorylate downstream targets in a signal transduction cascade, eventually leading to cell cycle arrest. A class of checkpoint mediator proteins including BRCA1, MDC1, and 53BP1 has also been identified. [54] These proteins seem to be required for transmitting the checkpoint activation signal to downstream proteins.

    DNA damage checkpoint is a signal transduction pathway that blocks cell cycle progression in G1, G2 and metaphase and slows down the rate of S phase progression when DNA is damaged. It leads to a pause in cell cycle allowing the cell time to repair the damage before continuing to divide.

    Checkpoint Proteins can be separated into four groups: phosphatidylinositol 3-kinase (PI3K)-like protein kinase, proliferating cell nuclear antigen (PCNA)-like group, two serine/threonine(S/T) kinases and their adaptors. Central to all DNA damage induced checkpoints responses is a pair of large protein kinases belonging to the first group of PI3K-like protein kinases-the ATM (Ataxia telangiectasia mutated) and ATR (Ataxia- and Rad-related) kinases, whose sequence and functions have been well conserved in evolution. All DNA damage response requires either ATM or ATR because they have the ability to bind to the chromosomes at the site of DNA damage, together with accessory proteins that are platforms on which DNA damage response components and DNA repair complexes can be assembled.

    An important downstream target of ATM and ATR is p53, as it is required for inducing apoptosis following DNA damage. [55] The cyclin-dependent kinase inhibitor p21 is induced by both p53-dependent and p53-independent mechanisms and can arrest the cell cycle at the G1/S and G2/M checkpoints by deactivating cyclin/cyclin-dependent kinase complexes. [56]

    The prokaryotic SOS response Edit

    The SOS response is the changes in gene expression in Escherichia coli and other bacteria in response to extensive DNA damage. The prokaryotic SOS system is regulated by two key proteins: LexA and RecA. The LexA homodimer is a transcriptional repressor that binds to operator sequences commonly referred to as SOS boxes. In Escherichia coli it is known that LexA regulates transcription of approximately 48 genes including the lexA and recA genes. [57] The SOS response is known to be widespread in the Bacteria domain, but it is mostly absent in some bacterial phyla, like the Spirochetes. [58] The most common cellular signals activating the SOS response are regions of single-stranded DNA (ssDNA), arising from stalled replication forks or double-strand breaks, which are processed by DNA helicase to separate the two DNA strands. [41] In the initiation step, RecA protein binds to ssDNA in an ATP hydrolysis driven reaction creating RecA–ssDNA filaments. RecA–ssDNA filaments activate LexA autoprotease activity, which ultimately leads to cleavage of LexA dimer and subsequent LexA degradation. The loss of LexA repressor induces transcription of the SOS genes and allows for further signal induction, inhibition of cell division and an increase in levels of proteins responsible for damage processing.

    In Escherichia coli, SOS boxes are 20-nucleotide long sequences near promoters with palindromic structure and a high degree of sequence conservation. In other classes and phyla, the sequence of SOS boxes varies considerably, with different length and composition, but it is always highly conserved and one of the strongest short signals in the genome. [58] The high information content of SOS boxes permits differential binding of LexA to different promoters and allows for timing of the SOS response. The lesion repair genes are induced at the beginning of SOS response. The error-prone translesion polymerases, for example, UmuCD'2 (also called DNA polymerase V), are induced later on as a last resort. [59] Once the DNA damage is repaired or bypassed using polymerases or through recombination, the amount of single-stranded DNA in cells is decreased, lowering the amounts of RecA filaments decreases cleavage activity of LexA homodimer, which then binds to the SOS boxes near promoters and restores normal gene expression.

    Eukaryotic transcriptional responses to DNA damage Edit

    Eukaryotic cells exposed to DNA damaging agents also activate important defensive pathways by inducing multiple proteins involved in DNA repair, cell cycle checkpoint control, protein trafficking and degradation. Such genome wide transcriptional response is very complex and tightly regulated, thus allowing coordinated global response to damage. Exposure of yeast Saccharomyces cerevisiae to DNA damaging agents results in overlapping but distinct transcriptional profiles. Similarities to environmental shock response indicates that a general global stress response pathway exist at the level of transcriptional activation. In contrast, different human cell types respond to damage differently indicating an absence of a common global response. The probable explanation for this difference between yeast and human cells may be in the heterogeneity of mammalian cells. In an animal different types of cells are distributed among different organs that have evolved different sensitivities to DNA damage. [60]

    In general global response to DNA damage involves expression of multiple genes responsible for postreplication repair, homologous recombination, nucleotide excision repair, DNA damage checkpoint, global transcriptional activation, genes controlling mRNA decay, and many others. A large amount of damage to a cell leaves it with an important decision: undergo apoptosis and die, or survive at the cost of living with a modified genome. An increase in tolerance to damage can lead to an increased rate of survival that will allow a greater accumulation of mutations. Yeast Rev1 and human polymerase η are members of [Y family translesion DNA polymerases present during global response to DNA damage and are responsible for enhanced mutagenesis during a global response to DNA damage in eukaryotes. [41]

    Pathological effects of poor DNA repair Edit

    Experimental animals with genetic deficiencies in DNA repair often show decreased life span and increased cancer incidence. [15] For example, mice deficient in the dominant NHEJ pathway and in telomere maintenance mechanisms get lymphoma and infections more often, and, as a consequence, have shorter lifespans than wild-type mice. [61] In similar manner, mice deficient in a key repair and transcription protein that unwinds DNA helices have premature onset of aging-related diseases and consequent shortening of lifespan. [62] However, not every DNA repair deficiency creates exactly the predicted effects mice deficient in the NER pathway exhibited shortened life span without correspondingly higher rates of mutation. [63]

    If the rate of DNA damage exceeds the capacity of the cell to repair it, the accumulation of errors can overwhelm the cell and result in early senescence, apoptosis, or cancer. Inherited diseases associated with faulty DNA repair functioning result in premature aging, [15] increased sensitivity to carcinogens, and correspondingly increased cancer risk (see below). On the other hand, organisms with enhanced DNA repair systems, such as Deinococcus radiodurans, the most radiation-resistant known organism, exhibit remarkable resistance to the double-strand break-inducing effects of radioactivity, likely due to enhanced efficiency of DNA repair and especially NHEJ. [64]

    Longevity and caloric restriction Edit

    A number of individual genes have been identified as influencing variations in life span within a population of organisms. The effects of these genes is strongly dependent on the environment, in particular, on the organism's diet. Caloric restriction reproducibly results in extended lifespan in a variety of organisms, likely via nutrient sensing pathways and decreased metabolic rate. The molecular mechanisms by which such restriction results in lengthened lifespan are as yet unclear (see [65] for some discussion) however, the behavior of many genes known to be involved in DNA repair is altered under conditions of caloric restriction. Several agents reported to have anti-aging properties have been shown to attenuate constitutive level of mTOR signaling, an evidence of reduction of metabolic activity, and concurrently to reduce constitutive level of DNA damage induced by endogenously generated reactive oxygen species. [66]

    For example, increasing the gene dosage of the gene SIR-2, which regulates DNA packaging in the nematode worm Caenorhabditis elegans, can significantly extend lifespan. [67] The mammalian homolog of SIR-2 is known to induce downstream DNA repair factors involved in NHEJ, an activity that is especially promoted under conditions of caloric restriction. [68] Caloric restriction has been closely linked to the rate of base excision repair in the nuclear DNA of rodents, [69] although similar effects have not been observed in mitochondrial DNA. [70]

    The C. elegans gene AGE-1, an upstream effector of DNA repair pathways, confers dramatically extended life span under free-feeding conditions but leads to a decrease in reproductive fitness under conditions of caloric restriction. [71] This observation supports the pleiotropy theory of the biological origins of aging, which suggests that genes conferring a large survival advantage early in life will be selected for even if they carry a corresponding disadvantage late in life.

    Hereditary DNA repair disorders Edit

    Defects in the NER mechanism are responsible for several genetic disorders, including:

      : hypersensitivity to sunlight/UV, resulting in increased skin cancer incidence and premature aging : hypersensitivity to UV and chemical agents : sensitive skin, brittle hair and nails

    Mental retardation often accompanies the latter two disorders, suggesting increased vulnerability of developmental neurons.

    Other DNA repair disorders include:

      : premature aging and retarded growth : sunlight hypersensitivity, high incidence of malignancies (especially leukemias). : sensitivity to ionizing radiation and some chemical agents

    All of the above diseases are often called "segmental progerias" ("accelerated aging diseases") because their victims appear elderly and suffer from aging-related diseases at an abnormally young age, while not manifesting all the symptoms of old age.

    Other diseases associated with reduced DNA repair function include Fanconi anemia, hereditary breast cancer and hereditary colon cancer.

    Because of inherent limitations in the DNA repair mechanisms, if humans lived long enough, they would all eventually develop cancer. [72] [73] There are at least 34 Inherited human DNA repair gene mutations that increase cancer risk. Many of these mutations cause DNA repair to be less effective than normal. In particular, Hereditary nonpolyposis colorectal cancer (HNPCC) is strongly associated with specific mutations in the DNA mismatch repair pathway. BRCA1 and BRCA2, two important genes whose mutations confer a hugely increased risk of breast cancer on carriers, [74] are both associated with a large number of DNA repair pathways, especially NHEJ and homologous recombination.

    Cancer therapy procedures such as chemotherapy and radiotherapy work by overwhelming the capacity of the cell to repair DNA damage, resulting in cell death. Cells that are most rapidly dividing – most typically cancer cells – are preferentially affected. The side-effect is that other non-cancerous but rapidly dividing cells such as progenitor cells in the gut, skin, and hematopoietic system are also affected. Modern cancer treatments attempt to localize the DNA damage to cells and tissues only associated with cancer, either by physical means (concentrating the therapeutic agent in the region of the tumor) or by biochemical means (exploiting a feature unique to cancer cells in the body). In the context of therapies targeting DNA damage response genes, the latter approach has been termed 'synthetic lethality'. [75]

    Perhaps the most well-known of these 'synthetic lethality' drugs is the poly(ADP-ribose) polymerase 1 (PARP1) inhibitor olaparib, which was approved by the Food and Drug Administration in 2015 for the treatment in women of BRCA-defective ovarian cancer. Tumor cells with partial loss of DNA damage response (specifically, homologous recombination repair) are dependent on another mechanism – single-strand break repair – which is a mechanism consisting, in part, of the PARP1 gene product. [76] Olaparib is combined with chemotherapeutics to inhibit single-strand break repair induced by DNA damage caused by the co-administered chemotherapy. Tumor cells relying on this residual DNA repair mechanism are unable to repair the damage and hence are not able to survive and proliferate, whereas normal cells can repair the damage with the functioning homologous recombination mechanism.

    Many other drugs for use against other residual DNA repair mechanisms commonly found in cancer are currently under investigation. However, synthetic lethality therapeutic approaches have been questioned due to emerging evidence of acquired resistance, achieved through rewiring of DNA damage response pathways and reversion of previously-inhibited defects. [77]

    DNA repair defects in cancer Edit

    It has become apparent over the past several years that the DNA damage response acts as a barrier to the malignant transformation of preneoplastic cells. [78] Previous studies have shown an elevated DNA damage response in cell-culture models with oncogene activation [79] and preneoplastic colon adenomas. [80] DNA damage response mechanisms trigger cell-cycle arrest, and attempt to repair DNA lesions or promote cell death/senescence if repair is not possible. Replication stress is observed in preneoplastic cells due to increased proliferation signals from oncogenic mutations. Replication stress is characterized by: increased replication initiation/origin firing increased transcription and collisions of transcription-replication complexes nucleotide deficiency increase in reactive oxygen species (ROS). [81]

    Replication stress, along with the selection for inactivating mutations in DNA damage response genes in the evolution of the tumor, [82] leads to downregulation and/or loss of some DNA damage response mechanisms, and hence loss of DNA repair and/or senescence/programmed cell death. In experimental mouse models, loss of DNA damage response-mediated cell senescence was observed after using a short hairpin RNA (shRNA) to inhibit the double-strand break response kinase ataxia telangiectasia (ATM), leading to increased tumor size and invasiveness. [80] Humans born with inherited defects in DNA repair mechanisms (for example, Li-Fraumeni syndrome) have a higher cancer risk. [83]

    The prevalence of DNA damage response mutations differs across cancer types for example, 30% of breast invasive carcinomas have mutations in genes involved in homologous recombination. [78] In cancer, downregulation is observed across all DNA damage response mechanisms (base excision repair (BER), nucleotide excision repair (NER), DNA mismatch repair (MMR), homologous recombination repair (HR), non-homologous end joining (NHEJ) and translesion DNA synthesis (TLS). [84] As well as mutations to DNA damage repair genes, mutations also arise in the genes responsible for arresting the cell cycle to allow sufficient time for DNA repair to occur, and some genes are involved in both DNA damage repair and cell cycle checkpoint control, for example ATM and checkpoint kinase 2 (CHEK2) – a tumor suppressor that is often absent or downregulated in non-small cell lung cancer. [85]

    HR NHEJ SSA FA BER NER MMR
    ATM x x x
    ATR x x x
    PAXIP x x
    RPA x x x
    BRCA1 x x
    BRCA2 x x
    RAD51 x x
    RFC x x x
    XRCC1 x x
    PCNA x x x
    PARP1 x x
    ERCC1 x x x x
    MSH3 x x x

    Table: Genes involved in DNA damage response pathways and frequently mutated in cancer (HR = homologous recombination NHEJ = non-homologous end joining SSA = single-strand annealing FA = fanconi anemia pathway BER = base excision repair NER = nucleotide excision repair MMR = mismatch repair)

    Epigenetic DNA repair defects in cancer Edit

    Classically, cancer has been viewed as a set of diseases that are driven by progressive genetic abnormalities that include mutations in tumour-suppressor genes and oncogenes, and chromosomal aberrations. However, it has become apparent that cancer is also driven by epigenetic alterations. [86]

    Epigenetic alterations refer to functionally relevant modifications to the genome that do not involve a change in the nucleotide sequence. Examples of such modifications are changes in DNA methylation (hypermethylation and hypomethylation) and histone modification, [87] changes in chromosomal architecture (caused by inappropriate expression of proteins such as HMGA2 or HMGA1) [88] and changes caused by microRNAs. Each of these epigenetic alterations serves to regulate gene expression without altering the underlying DNA sequence. These changes usually remain through cell divisions, last for multiple cell generations, and can be considered to be epimutations (equivalent to mutations).

    While large numbers of epigenetic alterations are found in cancers, the epigenetic alterations in DNA repair genes, causing reduced expression of DNA repair proteins, appear to be particularly important. Such alterations are thought to occur early in progression to cancer and to be a likely cause of the genetic instability characteristic of cancers. [89] [90] [91]

    Reduced expression of DNA repair genes causes deficient DNA repair. When DNA repair is deficient DNA damages remain in cells at a higher than usual level and these excess damages cause increased frequencies of mutation or epimutation. Mutation rates increase substantially in cells defective in DNA mismatch repair [92] [93] or in homologous recombinational repair (HRR). [94] Chromosomal rearrangements and aneuploidy also increase in HRR defective cells. [95]

    Higher levels of DNA damage not only cause increased mutation, but also cause increased epimutation. During repair of DNA double strand breaks, or repair of other DNA damages, incompletely cleared sites of repair can cause epigenetic gene silencing. [96] [97]

    Deficient expression of DNA repair proteins due to an inherited mutation can cause increased risk of cancer. Individuals with an inherited impairment in any of 34 DNA repair genes (see article DNA repair-deficiency disorder) have an increased risk of cancer, with some defects causing up to a 100% lifetime chance of cancer (e.g. p53 mutations). [98] However, such germline mutations (which cause highly penetrant cancer syndromes) are the cause of only about 1 percent of cancers. [99]

    Frequencies of epimutations in DNA repair genes Edit

    Deficiencies in DNA repair enzymes are occasionally caused by a newly arising somatic mutation in a DNA repair gene, but are much more frequently caused by epigenetic alterations that reduce or silence expression of DNA repair genes. For example, when 113 colorectal cancers were examined in sequence, only four had a missense mutation in the DNA repair gene MGMT, while the majority had reduced MGMT expression due to methylation of the MGMT promoter region (an epigenetic alteration). [100] Five different studies found that between 40% and 90% of colorectal cancers have reduced MGMT expression due to methylation of the MGMT promoter region. [101] [102] [103] [104] [105]

    Similarly, out of 119 cases of mismatch repair-deficient colorectal cancers that lacked DNA repair gene PMS2 expression, PMS2 was deficient in 6 due to mutations in the PMS2 gene, while in 103 cases PMS2 expression was deficient because its pairing partner MLH1 was repressed due to promoter methylation (PMS2 protein is unstable in the absence of MLH1). [106] In the other 10 cases, loss of PMS2 expression was likely due to epigenetic overexpression of the microRNA, miR-155, which down-regulates MLH1. [107]

    In a further example, epigenetic defects were found in various cancers (e.g. breast, ovarian, colorectal and head and neck). Two or three deficiencies in the expression of ERCC1, XPF or PMS2 occur simultaneously in the majority of 49 colon cancers evaluated by Facista et al. [108]

    The chart in this section shows some frequent DNA damaging agents, examples of DNA lesions they cause, and the pathways that deal with these DNA damages. At least 169 enzymes are either directly employed in DNA repair or influence DNA repair processes. [109] Of these, 83 are directly employed in repairing the 5 types of DNA damages illustrated in the chart.

    Some of the more well studied genes central to these repair processes are shown in the chart. The gene designations shown in red, gray or cyan indicate genes frequently epigenetically altered in various types of cancers. Wikipedia articles on each of the genes highlighted by red, gray or cyan describe the epigenetic alteration(s) and the cancer(s) in which these epimutations are found. Review articles, [110] and broad experimental survey articles [111] [112] also document most of these epigenetic DNA repair deficiencies in cancers.

    Red-highlighted genes are frequently reduced or silenced by epigenetic mechanisms in various cancers. When these genes have low or absent expression, DNA damages can accumulate. Replication errors past these damages (see translesion synthesis) can lead to increased mutations and, ultimately, cancer. Epigenetic repression of DNA repair genes in accurate DNA repair pathways appear to be central to carcinogenesis.

    The two gray-highlighted genes RAD51 and BRCA2, are required for homologous recombinational repair. They are sometimes epigenetically over-expressed and sometimes under-expressed in certain cancers. As indicated in the Wikipedia articles on RAD51 and BRCA2, such cancers ordinarily have epigenetic deficiencies in other DNA repair genes. These repair deficiencies would likely cause increased unrepaired DNA damages. The over-expression of RAD51 and BRCA2 seen in these cancers may reflect selective pressures for compensatory RAD51 or BRCA2 over-expression and increased homologous recombinational repair to at least partially deal with such excess DNA damages. In those cases where RAD51 or BRCA2 are under-expressed, this would itself lead to increased unrepaired DNA damages. Replication errors past these damages (see translesion synthesis) could cause increased mutations and cancer, so that under-expression of RAD51 or BRCA2 would be carcinogenic in itself.

    Cyan-highlighted genes are in the microhomology-mediated end joining (MMEJ) pathway and are up-regulated in cancer. MMEJ is an additional error-prone inaccurate repair pathway for double-strand breaks. In MMEJ repair of a double-strand break, an homology of 5–25 complementary base pairs between both paired strands is sufficient to align the strands, but mismatched ends (flaps) are usually present. MMEJ removes the extra nucleotides (flaps) where strands are joined, and then ligates the strands to create an intact DNA double helix. MMEJ almost always involves at least a small deletion, so that it is a mutagenic pathway. [24] FEN1, the flap endonuclease in MMEJ, is epigenetically increased by promoter hypomethylation and is over-expressed in the majority of cancers of the breast, [113] prostate, [114] stomach, [115] [116] neuroblastomas, [117] pancreas, [118] and lung. [119] PARP1 is also over-expressed when its promoter region ETS site is epigenetically hypomethylated, and this contributes to progression to endometrial cancer [120] and BRCA-mutated serous ovarian cancer. [121] Other genes in the MMEJ pathway are also over-expressed in a number of cancers (see MMEJ for summary), and are also shown in cyan.

    Genome-wide distribution of DNA repair in human somatic cells Edit

    Differential activity of DNA repair pathways across various regions of the human genome causes mutations to be very unevenly distributed within tumor genomes. [122] [123] In particular, the gene-rich, early-replicating regions of the human genome exhibit lower mutation frequencies than the gene-poor, late-replicating heterochromatin. One mechanism underlying this involves the histone modification H3K36me3, which can recruit mismatch repair proteins, [124] thereby lowering mutation rates in H3K36me3-marked regions. [125] Another important mechanism concerns nucleotide excision repair, which can be recruited by the transcription machinery, lowering somatic mutation rates in active genes [123] and other open chromatin regions. [126]

    The basic processes of DNA repair are highly conserved among both prokaryotes and eukaryotes and even among bacteriophages (viruses which infect bacteria) however, more complex organisms with more complex genomes have correspondingly more complex repair mechanisms. [127] The ability of a large number of protein structural motifs to catalyze relevant chemical reactions has played a significant role in the elaboration of repair mechanisms during evolution. For an extremely detailed review of hypotheses relating to the evolution of DNA repair, see. [128]

    The fossil record indicates that single-cell life began to proliferate on the planet at some point during the Precambrian period, although exactly when recognizably modern life first emerged is unclear. Nucleic acids became the sole and universal means of encoding genetic information, requiring DNA repair mechanisms that in their basic form have been inherited by all extant life forms from their common ancestor. The emergence of Earth's oxygen-rich atmosphere (known as the "oxygen catastrophe") due to photosynthetic organisms, as well as the presence of potentially damaging free radicals in the cell due to oxidative phosphorylation, necessitated the evolution of DNA repair mechanisms that act specifically to counter the types of damage induced by oxidative stress.

    Rate of evolutionary change Edit

    On some occasions, DNA damage is not repaired, or is repaired by an error-prone mechanism that results in a change from the original sequence. When this occurs, mutations may propagate into the genomes of the cell's progeny. Should such an event occur in a germ line cell that will eventually produce a gamete, the mutation has the potential to be passed on to the organism's offspring. The rate of evolution in a particular species (or, in a particular gene) is a function of the rate of mutation. As a consequence, the rate and accuracy of DNA repair mechanisms have an influence over the process of evolutionary change. [129] DNA damage protection and repair does not influence the rate of adaptation by gene regulation and by recombination and selection of alleles. On the other hand, DNA damage repair and protection does influence the rate of accumulation of irreparable, advantageous, code expanding, inheritable mutations, and slows down the evolutionary mechanism for expansion of the genome of organisms with new functionalities. The tension between evolvability and mutation repair and protection needs further investigation.

    A technology named clustered regularly interspaced short palindromic repeat (shortened to CRISPR-Cas9) was discovered in 2012. The new technology allows anyone with molecular biology training to alter the genes of any species with precision, by inducing DNA damage at a specific point and then altering DNA repair mechanisms to insert new genes. [130] It is cheaper, more efficient, and more precise than other technologies. With the help of CRISPR–Cas9, parts of a genome can be edited by scientists by removing, adding, or altering parts in a DNA sequence.


    Genetic Algorithms

    Evolution is well understood as a theory when it comes to biology. Organisms compete against each other for resources and therefore survival. Over time, through breeding and mutations, organisms adapt to gain competitive advantage within their environment. Those organisms that do well, survive and pass on their genetic legacy, while the others perish. With a relatively simple strategy, the results are impressive.

    Genetic Algorithms (GA) are a computer based problem solving strategy based on this evolutionary strategy. Potential solutions are forced to compete within an environment, resulting in better solutions over time. One of the key benefits of Genetic Algorithms is that the problem solver needs only to know how to evaluate a potential solution, not how to build the optimal one. This becomes increasingly important as the problem complexity rises because it becomes increasingly difficult to create an accurate model for the solution. In addition, the methods used by Genetic Algorithms model those used in human problem solving.

    Through an intelligent search strategy, a Genetic Algorithm can very efficiently search the solution space for a given problem and thus arrive at a good solution. By using an appropriate variety of mutation and crossover strategies, one can ensure that localized maxima and minima do not take over the population and therefore appear to be the proper solution to the problem. Traditional model-based approaches to solving a problem are bound by the quality and accuracy of the model. However, since a Genetic Algorithm does not have a comprehensive model of the solution space, the quality of the solutions is based on the accuracy of the evaluation criteria and mix of crossovers and mutations which explore the solution space. This is the Genetic Algorithm’s greatest strength. It is far easier to establish a set of evaluation criteria than to create a representative model directed toward achieving a solution.


    Chromosomes in the Cell

    Deletion Errors

    Sometimes a piece of chromosome breaks off, resulting in a deletion of genetic material. The effects of the loss of a portion of a chromosome depend on the particular genes lost. One of the earliest deletions noted with staining techniques was the loss of a portion of the short arm of chromosome 5. Affected infants have a rounded, moonlike face and utter feeble, plaintive cries described as similar to the mewing of a cat, and the disorder is named cri du chat (French, “cat cry”) syndrome. The cry disappears with time as the larynx improves and is rarely heard after the first year of life. The facial features also change with age, and the moon-shaped face becomes long and thin. Most patients survive beyond childhood, but they rank among the most profoundly retarded (IQ usually <20). Examples of deletion syndromes are shown in Table 2-2 .

    Deletions of varied types, notably interstitial and terminal, played a role in delineating the segment of chromosome 21 responsible for Down syndrome. Deletions of different segments of one of the long arms of chromosome 21 in trisomy 21 individuals (resulting in partial trisomy) have made it possible to identify the chromosome region responsible for the phenotypic features of Down syndrome. The “Down syndrome critical region” has been identified as a 5- to 10-Mb region of the chromosome and encompasses bands 21q22.2 to 21q22.3.


    Infectious virus hidden in chromosomes can be passed from parents to children

    Human herpesvirus 6 (HHV-6) infects nearly 100 percent of humans in early childhood, and the infection then lasts for the rest of a person's life. Now, a team led by Peter Medveczky, MD, a professor in the Department of Molecular Medicine at the University of South Florida (USF), has discovered that in some individuals, HHV-6 causes such a permanent infection by inserting or "integrating" its DNA into human chromosomes. From this harbor, the viral DNA cannot be eliminated by the immune system.

    The paper describing this research was published online March 8 in Proceedings of the National Academy of Sciences.

    The USF team also confirmed preliminary results by other investigators that, a long time ago, the virus inserted its DNA into the DNA of human sperm and egg cells. As a result, some people (about 1 percent of people in the U.S.) are born with the virus's DNA in every cell in their body. Indeed, HHV-6 is the first functional virus of any type reported to be passed through the human germ line.

    The team presented clear evidence that the virus can insert its DNA specifically into telomeres -- structures at the ends of each chromosome that play key roles in both aging and cancer.

    Finally, the team showed that the chromosomally integrated HHV-6 (CIHHV-6) genomes can be reactivated to an infectious form.

    The findings are a surprise, since other human herpesviruses cause permanent infection by a different mechanism. The round up their DNA into a little circle that resides inside the nucleus of the cell: they do not insert their DNA into the chromosomes.

    There are many unanswered questions that the USF team hopes to sort out. "We would like to know whether the location of the integration has an impact on pathology," Dr. Medveczky said. "We'd also like to know more about which drugs can provoke reactivation in patients that carry this virus in every cell. It would be important for these patients to avoid drugs that may reactivate the virus."

    "This is an exciting and provocative series of observations. The questions raised by this work will keep herpes virologists busy for years," predicted HHV-6 expert Phil Pellett, PhD of Wayne State University.

    HHV-6 was discovered in 1986 in the laboratory of Dr. Robert C. Gallo at the National Cancer Institute after Gallo asked his co-workers to look for a herpesvirus in AIDS lymphoma cases that might be triggering cancer. "In my mind these findings also should stimulate further studies on a possible role of HHV-6 in some cancers as suggested by others who have found a possible link to some lymphomas," Dr. Gallo commented. "However, clearly more work will be needed to advance any conclusion in this regard."

    HHV-6 causes roseola, a generally benign rash and fever in infants. The virus can reactivate in individuals with suppressed immune systems, sometimes causing serious consequences such as encephalitis, hepatitis, myocarditis, and pneumonia.

    Recent research has suggested that HHV-6 may also be associated with diseases in people with apparently healthy immune systems: encephalitis, mesial temporal lobe epilepsy, multiple sclerosis, myocarditis, and idiopathic cardiomyopathy. While there is no proof that the virus plays a causal role in these diseases, the virus has been found more often in the diseased tissue than in healthy tissue.

    Previous studies had used a visual technique called fluorescence in situ hybridization (FISH), which showed that the viral DNA was present at the same location (near the telomeres) of the same chromosome in both parent and child. This strongly suggested but did not prove that the virus was inherited through the germ line in these children. By determining the DNA sequence of the ends of the chromosome, the Medveczky team clearly demonstrated that the HHV-6 genome was integrated into telomere DNA. The team also showed that HHV-6 DNA, unlike other human herpesviruses, does not curl into a circle inside the nucleus.

    The great majority of people, however, do not inherit HHV-6 DNA from their parents and do not have it in every cell of their body. Yet nearly everyone becomes permanently infected with the virus. So Medveczky and colleagues wondered if the virus might take up permanent residence in the body by integrating its DNA into the chromosomes of just some cells.

    To examine this possibility, the investigators took cells that had never been exposed to HHV-6 and infected them with HHV-6 that had been engineered to make infected cells glow bright green. Sure enough, once the infection died down, the green cells contained HHV-6 DNA integrated into the ends of the chromosomes. When the investigators stimulated the cells with chemicals known to activate other herpesviruses, cells with integrated viral DNA began producing infectious virus. It will be important to learn whether a similar process occurs during the form of HHV-6 infection that occurs in most individuals.

    For the approximately 1 percent of the population born with viral DNA in every cell in their body, several questions arise. Are such people more prone to diseases because they have a greater risk of viral reactivation? If so, which diseases? If a person is born with viral proteins present from birth, would that person's immune system be "fooled" into thinking that the virus was not foreign and need not be attacked? If so, is that a bad thing or a good thing for a person's health? Finally, the virus inserts itself into the telomeres and could theoretically disrupt the function of the telomeres. Since the telomeres are important in cellular aging and in cancer, could the insertion of viral DNA in the telomeres have any effect on a cell's tendency to age or to turn cancerous?

    While unique among known human herpesviruses, the capacity of HHV-6 to integrate into human chromosomes is not unique in nature. A herpesvirus that infects chickens, called Marek's disease virus, appears to behave the same way. Interestingly, although the viruses are not otherwise closely related, the DNA sequence used by Marek's disease virus to integrate into chicken chromosomes is remarkably similar to the DNA sequence used for chromosomal integration by HHV-6.

    Doctoral student Jesse Arbuckle and research associate Maria Medveczky, both of the USF Department of Molecular Medicine, were lead authors of the study. Other contributing authors were from Bioworld Consulting Laboratories, the HHV-6 Foundation, University of Minnesota, University of Brussels, Stanford University School of Medicine and Harvard Medical School.

    The USF study was funded by the HHV-6 Foundation, a non-profit organization that supports virology research, as well as by a grant from the National Institutes of Health.

    Story Source:

    Materials provided by University of South Florida Health. Note: Content may be edited for style and length.


    An Introduction to Genetic Analysis. 7th edition.

    If two breaks occur in one chromosome, sometimes the region between the breaks rotates 180 degrees before rejoining with the two end fragments. Such an event creates a chromosomal mutation called an inversion. Unlike deletions and duplications, inversions do not change the overall amount of the genetic material, so inversions are generally viable and show no particular abnormalities at the phenotypic level. In some cases, one of the chromosome breaks is within a gene of essential function, and then that breakpoint acts as a lethal gene mutation linked to the inversion. In such a case, the inversion could not be bred to homozygosity. However, many inversions can be made homozygous furthermore, inversions can be detected in haploid organisms. In these cases, the breakpoint is clearly not in an essential region. Some of the possible outcomes of inversion at the DNA level are shown in Figure 17-14.

    Figure 17-14

    Effects of inversions at the DNA level. Genes are represented by A, B, C, and D. Template strand is dark green nontemplate strand is light green jagged lines indicate break in DNA. The letter P stands for promoter thick arrow indicates the position (more. )

    Most analyses of inversions use heterozygous inversions𠅍iploids in which one chromosome has the standard sequence and one carries the inversion. Microscopic observation of meioses in inversion heterozygotes reveals the location of the inverted segment because one chromosome twists once at the ends of the inversion to pair with the other, untwisted chromosome in this way the paired homologs form an inversion loop (Figure 17-15).

    Figure 17-15

    The chromosomes of inversion heterozygotes pair in a loop at meiosis. (a) Diagrammatic representation each chromosome is actually a pair of sister chromatids. (b) Electron micrographs of synaptonemal complexes at prophase I of meiosis in a mouse heterozygous (more. )

    The location of the centromere relative to the inverted segment determines the genetic behavior of the chromosome. If the centromere is outside the inversion, then the inversion is said to be paracentric, whereas inversions spanning the centromere are pericentric:

    How do inversions behave genetically? Crossing-over within the inversion loop of a paracentric inversion connects homologous centromeres in a dicentric bridge while also producing an acentric fragment𠅊 fragment without a centromere. Then, as the chromosomes separate in anaphase I, the centromeres remain linked by the bridge, which orients the centromeres so that the noncrossover chromatids lie farthest apart. The acentric fragment cannot align itself or move and is, consequently, lost. Tension eventually breaks the bridge, forming two chromosomes with terminal deletions (Figure 17-16). The gametes containing such deleted chromosomes may be inviable but, even if viable, the zygotes that they eventually form are inviable. Hence, a crossover event, which normally generates the recombinant class of meiotic products, instead produces lethal products. The overall result is a lower recombinant frequency. In fact, for genes within the inversion, the RF is zero. For genes flanking the inversion, the RF is reduced in proportion to the relative size of the inversion.

    Figure 17-16

    Meiotic products resulting from a single crossover within a paracentric inversion loop. Two nonsister chromatids cross over within the loop.

    Inversions affect recombination in another way too. Inversion heterozygotes often have mechanical pairing problems in the region of the inversion these pairing problems reduce the frequency of crossing-over and hence the recombinant frequency in the region.

    The net genetic effect of a pericentric inversion is the same as that of a paracentric one𠅌rossover products are not recovered𠅋ut for different reasons. In a pericentric inversion, because the centromeres are contained within the inverted region, the chromosomes that have crossed over disjoin in the normal fashion, without the creation of a bridge. However, the crossover produces chromatids that contain a duplication and a deficiency for different parts of the chromosome (Figure 17-17). In this case, if a nucleus carrying a crossover chromosome is fertilized, the zygote dies because of its genetic imbalance. Again, the result is the selective recovery of noncrossover chromosomes in viable progeny.

    Figure 17-17

    Meiotic products resulting from a meiosis with a single crossover within a pericentric inversion loop.

    MESSAGE

    Two mechanisms reduce the number of recombinant products among the progeny of inversion heterozygotes: elimination of the products of crossovers in the inversion loop and inhibition of pairing in the region of the inversion.

    It is worth adding a note about homozygous inversions. In such cases the homologous inverted chromosomes pair and cross over normally, there are no bridges, and the meiotic products are viable. However, an interesting effect is that the linkage map will show the inverted gene order.

    Geneticists use inversions to create duplications of specific chromosome regions for various experimental purposes. For example, consider a heterozygous pericentric inversion with one breakpoint at the tip (T) of the chromosome, as shown in Figure 17-18. A crossover in the loop produces a chromatid type in which the entire left arm is duplicated if the tip is nonessential, a duplication stock is generated for investigation. Another way to make a duplication (and a deficiency) is to use two paracentric inversions with overlapping breakpoints (Figure 17-19). A complex loop is formed, and a crossover within the inversion produces the duplication and the deletion. These manipulations are possible only in organisms with thoroughly mapped chromosomes for which large sets of standard rearrangements are available.

    Figure 17-18

    Generation of a viable nontandem duplication from a pericentric inversion close to a dispensable chromosome tip.

    Figure 17-19

    Generation of a nontandem duplication by crossing-over between two overlapping inversions.

    We have seen that genetic analysis and meiotic chromosome cytology are both good ways of detecting inversions. As with most rearrangements, there is also the possibility of detection through mitotic chromosome analysis. A key operational feature is to look for new arm ratios. Consider a chromosome that has mutated as follows:

    Note that the ratio of the long to the short arm has been changed from about 4 to about 1 by the pericentric inversion. Paracentric inversions do not alter the arm ratio, but they may be detected microscopically if banding or other chromosome landmarks are available.

    MESSAGE

    The main diagnostic features of inversions are inversion loops, reduction of recombinant frequency, and reduced fertility from unbalanced or deleted meiotic products, all observed in individuals heterozygous for inversions. Some inversions may be directly observed as an inverted arrangement of chromosomal landmarks.

    Inversions are found in about 2 percent of humans. The heterozygous inversion carriers generally show no adverse phenotype but produce the expected array of abnormal meiotic products from crossing-over in the inversion loop. Let us consider pericentric inversions as an example. Persons heterozygous for pericentric inversions produce offspring with the duplication�letion chromosomes predicted these offspring show varying degrees of abnormalities depending on the lengths of the chromosome regions affected. Some phenotypes caused by duplication�letion chromosomes are so abnormal as to be incapable of survival to birth and are lost as spontaneous abortions. However, there is a way to study the abnormal meiotic products that does not depend on survival to term. Human sperm placed in contact with unfertilized eggs of the golden hamster penetrate the eggs but fail to fertilize them. The sperm nucleus does not fuse with the egg nucleus, and, if the cell is prepared for cytogenetic examination, the human chromosomes are easily visible as a distinct group (Figure 17-20). This technique makes it possible to study the chromosomal products of a male meiosis directly and is particularly useful in the study of meiotic products of men who have chromosome mutations.

    Figure 17-20

    Human sperm and hamster oocytes are fused to permit study of the chromosomes in the meiotic products of human males. (After original art by Renພ Martin.)

    In one case, a man heterozygous for an inversion of chromosome 3 underwent sperm analysis. The inversion was a large one with a high potential for crossing-over in the loop. Four chromosome 3 types were found in the man’s sperm—normal, inversion, and two recombinant types (Figure 17-21). The sperm contained the four types in the following frequencies:

    Figure 17-21

    (a) Four different chromosomes 3 found in sperm of a man heterozygous for a large pericentric inversion. The duplication-deletion types result from a crossover in the inversion loop. (b) Two complete sperm chromosome sets containing the two duplication�letion (more. )

    The duplication-q�letion-p recombinant chromosome had been observed previously in several abnormal children, but the duplication-p�letion-q type had never been seen, and probably zygotes receiving it are too abnormal to survive to term. Presumably, deletion of the larger q fragment has more severe consequences than deletion of the smaller p fragment.

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    4. The balancer map

    Over half the C. elegans genome is covered by reliable, tested balancers (Figure 7). Well-balanced regions include virtually all of LG I, the right 65% of LG II, all of LG III, the right half of LG IV, the left 66% of LG V, and the right 80% of LG X (based on genetic, not physical, extents of each chromosome). Incompletely balanced regions include most of the remaining areas. Balancers may or may not include the physical ends of chromosomes. When drawn or referred to as including the end, it means only that the most distal genetic marker appears to be balanced.