View source for Biology:Double-strand break repair model

[[File:Double-strand break repair pathway models.png|thumb|Various pathways for double-strand break repair. [[Biology:Non-homologous end joining|NHEJ]] in this article refers to cNHEJ. MMEJ in this article refers to a-EJ. |345x345px]]
A '''double-strand break repair model''' refers to the various models of pathways that cells undertake to repair [[Biology:Double-strand breaks|double strand-breaks]] (DSB). DSB repair is an important cellular process, as the accumulation of unrepaired DSB could lead to chromosomal rearrangements, tumorigenesis or even cell death.<ref name=":0" /> In human cells, there are two main DSB repair mechanisms: [[Biology:Homologous recombination|Homologous recombination]] (HR) and [[Biology:Non-homologous end joining|non-homologous end joining]] (NHEJ). HR relies on undamaged template DNA as reference to repair the DSB, resulting in the restoration of the original sequence.<ref name=":11">{{cite journal | vauthors = Mao Z, Bozzella M, Seluanov A, Gorbunova V | title = Comparison of nonhomologous end joining and homologous recombination in human cells | journal = DNA Repair | volume = 7 | issue = 10 | pages = 1765–1771 | date = October 2008 | pmid = 18675941 | pmc = 2695993 | doi = 10.1016/j.dnarep.2008.06.018 }}</ref> NHEJ modifies and ligates the damaged ends regardless of homology.<ref name=":11" /> In terms of DSB repair pathway choice, most mammalian cells appear to favor NHEJ rather than HR. This is because the employment of HR may lead to [[Biology:Deletion (genetics)|gene deletion]] or amplification in cells which contains repetitive sequences.<ref name=":0">{{cite journal | vauthors = Featherstone C, Jackson SP | title = DNA double-strand break repair | language = English | journal = Current Biology | volume = 9 | issue = 20 | pages = R759–R761 | date = October 1999 | pmid = 10531043 | doi = 10.1016/S0960-9822(00)80005-6 | s2cid = 1941783 | doi-access = free }}</ref> In terms of repair models in the [[Biology:Cell cycle|cell cycle]], HR is only possible during the [[Biology:S phase|S]] and [[Biology:G2 phase|G2 phase]]s, while NHEJ can occur throughout whole process.<ref name=":2">{{cite journal | vauthors = Scully R, Panday A, Elango R, Willis NA | title = DNA double-strand break repair-pathway choice in somatic mammalian cells | journal = Nature Reviews. Molecular Cell Biology | volume = 20 | issue = 11 | pages = 698–714 | date = November 2019 | pmid = 31263220 | pmc = 7315405 | doi = 10.1038/s41580-019-0152-0 }}</ref> These repair pathways are all regulated by the overarching DNA damage response mechanism.<ref name=":15" /> Besides HR and NHEJ, there are also other repair models which exists in cells. Some are categorized under HR, such as [[Biology:Synthesis-dependent strand annealing|synthesis-dependent strain annealing]], break-induced replication, and single-strand annealing; while others are an entirely alternate repair model, namely, the pathway [[Biology:Microhomology-mediated end joining|microhomology-mediated end joining]] (MMEJ).<ref name=":14" />

== Causes ==
DSB can occur naturally due to the presence of reactive species generated by metabolism, and various external factors (e.g. [[Physics:Ionizing radiation|ionizing radiation]] or chemotherapeutic drugs).<ref name=":0" />

In mammalian cells, there are numerous cellular processes that induce DSB. Firstly, DNA topological strain from [[Biology:Topoisomerase|topoisomerase]] during normal cell growth can cause the majority a cell’s DSB.<ref>{{cite journal | vauthors = Tan XY, Huen MS | title = Perfecting DNA double-strand break repair on transcribed chromatin | journal = Essays in Biochemistry | volume = 64 | issue = 5 | pages = 705–719 | date = October 2020 | pmid = 32309851 | doi = 10.1042/EBC20190094 | s2cid = 216030185 }}</ref> Secondly, cellular processes such as [[Biology:Meiosis|meiosis]] and the maturation of [[Biology:Antibodies|antibodies]] can cause nuclease-induced DSB.<ref name=":1">{{cite journal | vauthors = Bhargava R, Onyango DO, Stark JM | title = Regulation of Single-Strand Annealing and its Role in Genome Maintenance | journal = Trends in Genetics | volume = 32 | issue = 9 | pages = 566–575 | date = September 2016 | pmid = 27450436 | pmc = 4992407 | doi = 10.1016/j.tig.2016.06.007 }}</ref> Thirdly, the cleavage of different DNA structures such as reversed or blocked DNA replication forks, [[Biology:R-loop|R-loop]]s and DNA interstrand crosslinks can also cause DSB.<ref name=":1" />

== Different models ==

=== Homologous recombination ===
[[Biology:Homologous recombination|Homologous recombination]] involves the exchange of DNA materials between homologous chromosomes. There are multiple pathways of HR to repair DSBs, which includes double-strand break repair (DSBR), [[Biology:Synthesis-dependent strand annealing|synthesis-dependent strand annealing]] (SDSA), break-induced replication (BIR), and single-strand annealing (SSA).<ref name=":3">{{cite book | vauthors = Sebesta M, Krejci L |title=DNA Replication, Recombination, and Repair |chapter=Mechanism of Homologous Recombination|date=2016|chapter-url=https://doi.org/10.1007/978-4-431-55873-6_4|work=DNA Replication, Recombination, and Repair: Molecular Mechanisms and Pathology|pages=73–109| veditors = Hanaoka F, Sugasawa K |place=Tokyo|publisher=Springer Japan|language=en|doi=10.1007/978-4-431-55873-6_4|isbn=978-4-431-55873-6|access-date=2021-03-31 }}</ref>

The regulation of HR in mammalian cells involves key HR proteins such as [[Biology:BRCA1|BRCA1]] and [[Biology:BRCA2|BRCA2]].<ref name=":4">{{cite journal | vauthors = Do AT, Brooks JT, Le Neveu MK, LaRocque JR | title = Double-strand break repair assays determine pathway choice and structure of gene conversion events in Drosophila melanogaster | journal = G3 | volume = 4 | issue = 3 | pages = 425–432 | date = March 2014 | pmid = 24368780 | pmc = 3962482 | doi = 10.1534/g3.113.010074 }}</ref> And as mentioned, since HR can lead to aggressive chromosomal rearrangement, loss of genetic information that could contribute to cell death, it explains why HR is strictly regulated.<ref name=":3" />

==== Double-strand break repair ====
[[File:Double-strand break repair models that act via homologous recombination.png|thumb|Three possible sub-pathways for a double-strand break to repair via homologous recombination: Gene conversion, BIR and SDSA. The gene conversion is referring to the double-strand break repair model. The other sub-pathway is the synthesis-dependent strain annealing. SSA is the fourth sub-pathway and it is not shown in this diagram.  |411x411px]]
HR repairs DSB by copying intact and homologous DNA molecules. The blunt ends of the DSB are processed into ssDNA with 3’ extensions, which allows [[Biology:RAD51|RAD51]] recombinase (eukaryotic homologue of prokaryotic [[Biology:RecA|RecA]]) to bind to it to form a nucleoprotein filament.<ref name=":2" /><ref name=":5">{{cite journal | vauthors = Modesti M, Kanaar R | title = Homologous recombination: from model organisms to human disease | journal = Genome Biology | volume = 2 | issue = 5 | pages = REVIEWS1014 | date = 2001-04-26 | pmid = 11387040 | pmc = 138934 | doi = 10.1186/gb-2001-2-5-reviews1014 | doi-access = free }}</ref> The function of the filament is to locate the template DNA and form a joint heteroduplex molecule. Other proteins such as RP-A protein and RAD52 also coordinate in the heteroduplex formation,<ref name=":5" /> the [[Biology:Replication protein A|RP-A]] protein has to be removed for the RAD51 to form the filament,<ref>{{cite journal | vauthors = Wright WD, Shah SS, Heyer WD | title = Homologous recombination and the repair of DNA double-strand breaks | language = English | journal = The Journal of Biological Chemistry | volume = 293 | issue = 27 | pages = 10524–10535 | date = July 2018 | pmid = 29599286 | doi = 10.1074/jbc.TM118.000372 | pmc = 6036207 | doi-access = free }}</ref> whereas the RAD52 is a key HR mediator.<ref name=":2" /> Afterwards, the 3’ ssDNA invades the template DNA, and displaces a DNA strand to form a D-loop. DNA polymerase and other accessory factors follows by replacing the missing DNA via DNA synthesis. Ligase then attaches the DNA strand break,<ref name=":5" /> resulting in the formation of 2 [[Biology:Holliday junction|Holliday junction]]s. The recombined DNA strands then undergoes resolution by cleavage. The orientation of the cleavage determines whether the resolution results in either cross-over or noncross-over products.<ref name=":12">{{cite journal | vauthors = Shah Punatar R, Martin MJ, Wyatt HD, Chan YW, West SC | title = Resolution of single and double Holliday junction recombination intermediates by GEN1 | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 114 | issue = 3 | pages = 443–450 | date = January 2017 | pmid = 28049850 | doi = 10.1073/pnas.1619790114 | pmc = 5255610 | bibcode = 2017PNAS..114..443S | doi-access = free }}</ref> Lastly, the strands finally separate and revert to its original form.

, the main pathway for resolution relies on the BTR (BLM helicase-TopoisomeraseIIIα-RMI1-RM2) complex, where it induces the resolution of the 2 Holliday junctions, but this pathway favors the noncross-over cleavage.<ref name=":12" />

==== Synthesis-dependent strain annealing ====
[[Biology:Synthesis-dependent strand annealing|Synthesis-dependent strain annealing]] is the most preferred repair mechanism in [[Biology:Somatic cell|somatic cell]]s.<ref name=":2" /> The pathway of SDSA is similar to DSBR until just after the D-loop formation.  Instead of forming Holliday junctions after DNA synthesis, the nascent strand dissociates via RETL1 helicase and anneals back to the other end of the resected strand.<ref name=":2" /><ref name=":4" /><ref>{{cite journal | vauthors = Currall BB, Chiang C, Talkowski ME, Morton CC | title = Mechanisms for Structural Variation in the Human Genome | journal = Current Genetic Medicine Reports | volume = 1 | issue = 2 | pages = 81–90 | date = June 2013 | pmid = 23730541 | pmc = 3665418 | doi = 10.1007/s40142-013-0012-8 }}</ref> This explains why SDSA results in a non-crossover pathway.<ref name=":2" /> The remaining gap is filled in and the nick is attached by the ligase.<ref name=":4" />

==== Break-induced replication ====
Although there is little research in regards of break-induced replication, it is known that it is a one-ended recombination mechanism, where only of the one ends of a DSB will be involved in strand invasion.<ref name=":13">{{cite journal | vauthors = Kraus E, Leung WY, Haber JE | title = Break-induced replication: a review and an example in budding yeast | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 98 | issue = 15 | pages = 8255–8262 | date = July 2001 | pmid = 11459961 | doi = 10.1073/pnas.151008198 | pmc = 37429 | bibcode = 2001PNAS...98.8255K | doi-access = free }}</ref> This means that unlike DSBR, BIR does not link back to the second DSB end after the strand invasion and replication.<ref name=":13" />

==== Single-strand annealing ====
Single-strand annealing involves homologous/repeated sequences flanking a DSB.<ref name=":1" /> The process starts with the key end resection factor CtlP, which mediates the end resection of DSBs, resulting in the formation of a 3' ssDNA extension. Meditated by RAD52, the flanking homologous sequences are annealed, and forms a synapse intermediate.<ref name=":1" /> Then, the nonhomologous 3’ extension is removed by the ERCC1-[[Biology:Non-homologous end-joining factor 1|XPF]] complex through endonucleolytic cleavage, with RAD52 increasing the efficiency of the ERCC1-XPF complex activity.<ref name=":1" /> It is only after the removal of 3’ ssDNA, where the polymerase will fill the missing gaps and the ligase to ligate the strands.<ref name=":1" /> Since SSA results in the deletion of repetitive sequences, this could potentially lead to error-prone repair.<ref name=":2" />

Single-strand annealing differs from SDSA and DSBR in numerous ways. For instance, the 3’ extension after the end resection in SSA anneals to the repeated/homologous sequences of the other end, whereas in other pathways the strand invasion to another homologous DNA template.<ref>{{cite journal | vauthors = Lok BH, Powell SN | title = Molecular pathways: understanding the role of Rad52 in homologous recombination for therapeutic advancement | journal = Clinical Cancer Research | volume = 18 | issue = 23 | pages = 6400–6406 | date = December 2012 | pmid = 23071261 | pmc = 3513650 | doi = 10.1158/1078-0432.CCR-11-3150 }}</ref> Moreover, SSA does not require [[Biology:RAD51|RAD51]], because it does not involve strand invasion, but rather the annealing of homologous sequences.<ref name=":2" />

=== Non-homologous end joining ===
[[Biology:Non-homologous end joining|Non-homologous end joining]] (NHEJ) is one of the major pathways in DSB repair besides HR.<ref>{{cite journal | vauthors = Radhakrishnan SK, Jette N, Lees-Miller SP | title = Non-homologous end joining: emerging themes and unanswered questions | journal = DNA Repair | volume = 17 | pages = 2–8 | date = May 2014 | pmid = 24582502 | pmc = 4084493 | doi = 10.1016/j.dnarep.2014.01.009 | series = Recent Developments in Non-Homologous End Joining }}</ref> The basic concept of NHEJ involves three steps. First, the ends of a DSB is captured by a group of enzymes. The enzymes then form a bridge which connects the DSB ends together, and is lastly followed by religation of the DNA strands.<ref name=":7">{{cite journal | vauthors = Weterings E, Chen DJ | title = The endless tale of non-homologous end-joining | journal = Cell Research | volume = 18 | issue = 1 | pages = 114–124 | date = January 2008 | pmid = 18166980 | doi = 10.1038/cr.2008.3 | s2cid = 2090745 | doi-access = free }}</ref> To initiate whole process, the Ku70/80 protein complex binds to the damaged ends of the DSB strands. This forms a preliminary scaffold which allows the recruitment of various NHEJ factors, such as the [[Biology:DNA-PKcs|DNA-dependent protein kinase catalytic subunit]] (DNA-PKcs), [[Biology:DNA ligase|DNA Ligase IV]] and X-ray cross complementing protein 4 (XRCC4) to form a bridge and bring both ends of the damaged DNA strands together.<ref>{{cite journal | vauthors = Uematsu N, Weterings E, Yano K, Morotomi-Yano K, Jakob B, Taucher-Scholz G, Mari PO, van Gent DC, Chen BP, Chen DJ | display-authors = 6 | title = Autophosphorylation of DNA-PKCS regulates its dynamics at DNA double-strand breaks | journal = The Journal of Cell Biology | volume = 177 | issue = 2 | pages = 219–229 | date = April 2007 | pmid = 17438073 | pmc = 2064131 | doi = 10.1083/jcb.200608077 }}</ref><ref>{{cite journal | vauthors = Mari PO, Florea BI, Persengiev SP, Verkaik NS, Brüggenwirth HT, Modesti M, Giglia-Mari G, Bezstarosti K, Demmers JA, Luider TM, Houtsmuller AB, van Gent DC | display-authors = 6 | title = Dynamic assembly of end-joining complexes requires interaction between Ku70/80 and XRCC4 | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 49 | pages = 18597–18602 | date = December 2006 | pmid = 17124166 | pmc = 1693708 | doi = 10.1073/pnas.0609061103 | bibcode = 2006PNAS..10318597M | doi-access = free }}</ref><ref>{{cite journal | vauthors = Costantini S, Woodbine L, Andreoli L, Jeggo PA, Vindigni A | title = Interaction of the Ku heterodimer with the DNA ligase IV/Xrcc4 complex and its regulation by DNA-PK | journal = DNA Repair | volume = 6 | issue = 6 | pages = 712–722 | date = June 2007 | pmid = 17241822 | doi = 10.1016/j.dnarep.2006.12.007 }}</ref><ref>{{cite journal | vauthors = Nick McElhinny SA, Snowden CM, McCarville J, Ramsden DA | title = Ku recruits the XRCC4-ligase IV complex to DNA ends | journal = Molecular and Cellular Biology | volume = 20 | issue = 9 | pages = 2996–3003 | date = May 2000 | pmid = 10757784 | pmc = 85565 | doi = 10.1128/MCB.20.9.2996-3003.2000 }}</ref> This is then followed by the processing of any non-ligatable DNA termini by a group of proteins including Artemis, [[Biology:PNKP|PNKP]], APLF and Ku, before the [[Biology:DNA repair protein XRCC4|XRCC4]] and DNA Ligase IV ligate the bridged DNA.<ref name=":7" /><ref>{{cite journal | vauthors = Davis AJ, Chen DJ | title = DNA double strand break repair via non-homologous end-joining | journal = Translational Cancer Research | volume = 2 | issue = 3 | pages = 130–143 | date = June 2013 | pmid = 24000320 | pmc = 3758668 | doi = 10.3978/j.issn.2218-676X.2013.04.02  }}</ref>

=== Microhomology-mediated end joining ===
[[Biology:Microhomology-mediated end joining|Microhomology-mediated end joining]] (MMEJ), also known as alt-non-homologous end joining, is another pathway to repair DSBs. The process of MMEJ can be summarized in five steps: the 5' to 3' cutting of DNA ends, annealing of microhomology, removing heterologous flaps, and ligation and synthesis of gap filling DNA.<ref name=":14">{{cite journal | vauthors = Sfeir A, Symington LS | title = Microhomology-Mediated End Joining: A Back-up Survival Mechanism or Dedicated Pathway? | journal = Trends in Biochemical Sciences | volume = 40 | issue = 11 | pages = 701–714 | date = November 2015 | pmid = 26439531 | pmc = 4638128 | doi = 10.1016/j.tibs.2015.08.006 }}</ref> It was found that the selection between MMEJ and NHEJ is mainly dependent on [[Biology:Ku (protein)|Ku]] levels and the concurrent cell cycle.<ref>{{cite journal | vauthors = Truong LN, Li Y, Shi LZ, Hwang PY, He J, Wang H, Razavian N, Berns MW, Wu X | display-authors = 6 | title = Microhomology-mediated End Joining and Homologous Recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 110 | issue = 19 | pages = 7720–7725 | date = May 2013 | pmid = 23610439 | pmc = 3651503 | doi = 10.1073/pnas.1213431110 | bibcode = 2013PNAS..110.7720T | doi-access = free }}</ref>

== The regulation of double-strand break repair pathways ==

=== DNA damage response ===
[[Biology:DNA repair|DNA damage response]] (DDR) is the overarching mechanism which mediates the cell's detection and response to DNA damage. This includes the process of detecting DSB within the cell, and the subsequent triggering and regulation of DSB repair pathways. Upstream detections of DNA damage via DDR will lead to the activation of downstream responses such as [[Biology:Cellular senescence|senescence]], [[Biology:Apoptosis|cell apoptosis]], halting [[Biology:Transcription|transcription]] and activating DNA repair mechanisms.<ref name=":15">{{cite journal | vauthors = Zhou BB, Elledge SJ | title = The DNA damage response: putting checkpoints in perspective | journal = Nature | volume = 408 | issue = 6811 | pages = 433–439 | date = November 2000 | pmid = 11100718 | doi = 10.1038/35044005 | bibcode = 2000Natur.408..433Z | s2cid = 4419141 }}</ref> Proteins such as the proteins ATM, ATR and DNA-dependent protein kinase (DNA-PK) are vital for the process of detection of DSB in DDR, and these proteins are recruited to the DSB site in the DNA.<ref name=":8">{{cite journal | vauthors = Blackford AN, Jackson SP | title = ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA Damage Response | journal = Molecular Cell | volume = 66 | issue = 6 | pages = 801–817 | date = June 2017 | pmid = 28622525 | doi = 10.1016/j.molcel.2017.05.015 | s2cid = 206997898 | doi-access = free }}</ref> In particular, ATM has been identified as the protein kinase in charge of the global meditation of cellular responses to DSB, which includes various DSB repair pathways.<ref name=":8" /> Following the recruitment of the aforementioned proteins to DNA damage sites, they will in turn trigger cellular responses and repair pathways to mitigate and repair the damage caused.<ref name=":15" /> In short, these vital upstream proteins and downstream repair pathways altogether forms the DDR, which plays a vital role in DSB repair pathways regulation.

===Fanconi anemia complex in one DNA damage response pathway===

[[File:Recombinational repair of DNA double-strand damage.jpg|thumb|300px]] 

The image in this section illustrates molecular steps in a DNA damage response pathway in which a Fanconi anemia complex is activated during repair of a double-strand break.  ATM (ATM) is also a [[Biology:Protein kinase|protein kinase]] that is recruited and activated by [[Biology:DNA repair#Double-strand breaks|DNA double-strand breaks]].  DNA double-strand damages
activate the [[Biology:FANC proteins|Fanconi anemia core complex]] (FANCA/B/C/E/F/G/L/M).<ref name="pmid20484397">{{cite journal |vauthors=D'Andrea AD |title=Susceptibility pathways in Fanconi's anemia and breast cancer |journal=N. Engl. J. Med. |volume=362 |issue=20 |pages=1909–19 |year=2010 |pmid=20484397 |pmc=3069698 |doi=10.1056/NEJMra0809889 |url=}}</ref>  The FA core complex [[Biology:Ubiquitin|monoubiquitinates]] the downstream targets FANCD2 and FANCI.<ref name="pmid19633289">{{cite journal |vauthors=Sobeck A, Stone S, Landais I, de Graaf B, Hoatlin ME |title=The Fanconi anemia protein FANCM is controlled by FANCD2 and the ATR/ATM pathways |journal=J. Biol. Chem. |volume=284 |issue=38 |pages=25560–8 |year=2009 |pmid=19633289 |pmc=2757957 |doi=10.1074/jbc.M109.007690 |url=}}</ref>   ATM activates (phosphorylates) [[Biology:CHEK2|CHEK2]] and [[Biology:FANCD2|FANCD2]]<ref name=Castillo>{{cite journal |vauthors=Castillo P, Bogliolo M, Surralles J |title=Coordinated action of the Fanconi anemia and ataxia telangiectasia pathways in response to oxidative damage |journal=DNA Repair (Amst.) |volume=10 |issue=5 |pages=518–25 |year=2011 |pmid=21466974 |doi=10.1016/j.dnarep.2011.02.007 |url=}}</ref>  CHEK2 phosphorylates BRCA1.<ref name="pmid21088254">{{cite journal |vauthors=Stolz A, Ertych N, Bastians H |title=Tumor suppressor CHK2: regulator of DNA damage response and mediator of chromosomal stability |journal=Clin. Cancer Res. |volume=17 |issue=3 |pages=401–5 |year=2011 |pmid=21088254 |doi=10.1158/1078-0432.CCR-10-1215 |url=|doi-access=free }}</ref>   Ubiquinated FANCD2 complexes with [[Biology:BRCA1|BRCA1]] and [[Biology:RAD51|RAD51]].<ref name="pmid12239151">{{cite journal |vauthors=Taniguchi T, Garcia-Higuera I, Andreassen PR, Gregory RC, Grompe M, D'Andrea AD |title=S-phase-specific interaction of the Fanconi anemia protein, FANCD2, with BRCA1 and RAD51 |journal=Blood |volume=100 |issue=7 |pages=2414–20 |year=2002 |pmid=12239151 |doi=10.1182/blood-2002-01-0278 |url=}}</ref>  The PALB2 protein acts as a hub,<ref name="pmid24998779">{{cite journal |vauthors=Park JY, Zhang F, Andreassen PR |title=PALB2: the hub of a network of tumor suppressors involved in DNA damage responses |journal=Biochim. Biophys. Acta |volume=1846 |issue=1 |pages=263–75 |year=2014 |pmid=24998779 |pmc=4183126 |doi=10.1016/j.bbcan.2014.06.003 |url=}}</ref> bringing together BRCA1, BRCA2 and RAD51 at the site of a DNA double-strand break, and also binds to RAD51C, a member of the RAD51 paralog complex RAD51B-[[Biology:RAD51C|RAD51C]]-RAD51D-XRCC2 (BCDX2).  The BCDX2 complex is responsible for RAD51 recruitment or stabilization at damage sites.<ref name=Chun>{{cite journal |vauthors=Chun J, Buechelmaier ES, Powell SN |title=Rad51 paralog complexes BCDX2 and CX3 act at different stages in the BRCA1-BRCA2-dependent homologous recombination pathway |journal=Mol. Cell. Biol. |volume=33 |issue=2 |pages=387–95 |year=2013 |pmid=23149936 |pmc=3554112 |doi=10.1128/MCB.00465-12 |url=}}</ref>  [[Biology:RAD51|RAD51]] plays a major role in [[Biology:Homologous recombination|homologous recombination]]al repair of DNA during double strand break repair. In this process, an ATP dependent DNA strand exchange takes place in which a template strand invades base-paired strands of homologous DNA molecules.  RAD51 is involved in the search for homology and strand pairing stages of the process.

=== Double-strand break repair pathway choice ===
As cells have developed various DSB repair models, it is said that specific pathways are favoured for their ability to repair DSB depending on the cellular context.<ref>{{cite journal | vauthors = Chapman JR, Taylor MR, Boulton SJ | title = Playing the end game: DNA double-strand break repair pathway choice | journal = Molecular Cell | volume = 47 | issue = 4 | pages = 497–510 | date = August 2012 | pmid = 22920291 | doi = 10.1016/j.molcel.2012.07.029 | doi-access = free }}</ref> These conditions include the type of DSB involved, the species of cells involved, and the stage of the cell cycle.<ref name=":9" />

==== In various types of DSB ====
Cells have evolved a multitude of DSB repair pathways in response to the various types of DSB.<ref name=":9">{{cite journal | vauthors = Shrivastav M, De Haro LP, Nickoloff JA | title = Regulation of DNA double-strand break repair pathway choice | journal = Cell Research | volume = 18 | issue = 1 | pages = 134–147 | date = January 2008 | pmid = 18157161 | doi = 10.1038/cr.2007.111 | s2cid = 20992607 | doi-access = free }}</ref> Hence, various pathways are favoured in different situations. For instance, frank DSB, which are DSB induced by substances like as [[Physics:Ionizing radiation|ionizing radiation]], and [[Biology:Nuclease|nuclease]]s, can be repaired by both HR and NHEJ. On the other hand, DSB due to replication fork collapse mainly favours HR.<ref name=":9" /><ref>{{cite journal | vauthors = Rothstein R, Michel B, Gangloff S | title = Replication fork pausing and recombination or "gimme a break" | journal = Genes & Development | volume = 14 | issue = 1 | pages = 1–10 | date = January 2000 | doi = 10.1101/gad.14.1.1 | pmid = 10640269 | s2cid = 40751623 | doi-access = free }}</ref>

==== In higher eukaryotes and yeast cells ====
It is said that the favoured pathway in a particular situations is also largely dependent on the species of the cell, the cell type, and [[Biology:Cell cycle|cell cycle]] phases; and are all modulated and triggered by different upstream regulatory proteins.<ref name=":9" /> As compared to [[Biology:Eukaryote|higher eukaryotes]], [[Biology:Yeast|yeast]] cells have adopted HR as the main repair pathway for DSB.<ref>{{cite journal | vauthors = Sugawara N, Haber JE | title = Characterization of double-strand break-induced recombination: homology requirements and single-stranded DNA formation | journal = Molecular and Cellular Biology | volume = 12 | issue = 2 | pages = 563–575 | date = February 1992 | pmid = 1732731 | pmc = 364230 | doi = 10.1128/MCB.12.2.563 }}</ref> Imprecise NHEJ, the primary pathway for NHEJ to repair "dirty" ends due to IR, was found to be inefficent at repairing DSB in yeast cells. It was hypothesized that this inefficiency as compared to mammalian cells is due to the lack of three vital NHEJ proteins, including [[Biology:DNA-PKcs|DNA-PKcs]], [[Biology:BRCA1|BRCA1]], and Artemis.<ref name=":9" /> Contrary to yests, higher eukaryotes has a much higher frequency and efficiency at adopting NHEJ pathways.<ref>{{cite journal | vauthors = Lin Y, Lukacsovich T, Waldman AS | title = Multiple pathways for repair of DNA double-strand breaks in mammalian chromosomes | journal = Molecular and Cellular Biology | volume = 19 | issue = 12 | pages = 8353–8360 | date = December 1999 | pmid = 10567560 | pmc = 84924 | doi = 10.1128/MCB.19.12.8353 }}</ref> Research hypothesize that this is due to the higher eukaryote's larger genome size, as it means that more NHEJ related proteins are encoded for NHEJ repair pathways; and a larger genome implies a challenging obstacle to find a homologous template for HR.<ref name=":9" />

==== In cell cycle ====
HR and NHEJ pathways are favoured in various phases of cell cycles for a multitude of factors. As [[Biology:S phase|S]] and [[Biology:G2 phase|G2 phase]]s of the cell cycle generate more [[Biology:Chromatid|chromatid]]s, the increased availability of template access for HR results in the up-regulation of the pathway.<ref>{{cite journal | vauthors = Dronkert ML, Beverloo HB, Johnson RD, Hoeijmakers JH, Jasin M, Kanaar R | title = Mouse RAD54 affects DNA double-strand break repair and sister chromatid exchange | journal = Molecular and Cellular Biology | volume = 20 | issue = 9 | pages = 3147–3156 | date = May 2000 | pmid = 10757799 | pmc = 85609 | doi = 10.1128/MCB.20.9.3147-3156.2000 }}</ref> This rise is further increased due to the activation of [[Biology:Cyclin-dependent kinase 1|CDK1]] and the increase of [[Biology:RAD51|RAD51]] and RAD52 levels during G1 phase.<ref name=":9" /><ref name=":10">{{cite journal | vauthors = Chen F, Nastasi A, Shen Z, Brenneman M, Crissman H, Chen DJ | title = Cell cycle-dependent protein expression of mammalian homologs of yeast DNA double-strand break repair genes Rad51 and Rad52 | journal = Mutation Research | volume = 384 | issue = 3 | pages = 205–211 | date = September 1997 | pmid = 9330616 | doi = 10.1016/S0921-8777(97)00020-7 }}</ref> Despite this, NHEJ not is inactive during the HR up-regulation. In fact, NHEJ was shown to be active throughout all stages of the cell cycle, and is favoured in G1 phase during low resection action intervals.<ref>{{cite journal | vauthors = Aylon Y, Liefshitz B, Kupiec M | title = The CDK regulates repair of double-strand breaks by homologous recombination during the cell cycle | journal = The EMBO Journal | volume = 23 | issue = 24 | pages = 4868–4875 | date = December 2004 | pmid = 15549137 | pmc = 535085 | doi = 10.1038/sj.emboj.7600469 }}</ref><ref>{{cite journal | vauthors = Ira G, Pellicioli A, Balijja A, Wang X, Fiorani S, Carotenuto W, Liberi G, Bressan D, Wan L, Hollingsworth NM, Haber JE, Foiani M | display-authors = 6 | title = DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1 | journal = Nature | volume = 431 | issue = 7011 | pages = 1011–1017 | date = October 2004 | pmid = 15496928 | pmc = 4493751 | doi = 10.1038/nature02964 | bibcode = 2004Natur.431.1011I }}</ref> This suggests the competition between HR and NHEJ for DSB repair in cells.<ref name=":10" /> It should be noted, however, that there is a shift of favour from NHEJ to HR when the cell cycle is progressing from G1 to S/G2 phases in eukaryotic cells.<ref name=":10" />

====During meiosis====

In [[Biology:Ploidy|diploid]] [[Biology:Eukaryote|eukaryotic organisms]], the events of [[Biology:Meiosis|meiosis]] can be viewed as occurring in three steps.  (1) Haploid [[Biology:Gamete|gamete]]s undergo syngamy/[[Biology:Fertilisation|fertilisation]] with the result that [[Biology:Chromosome|chromosome]] sets of different parental origin come together to share the same [[Biology:Cell nucleus|nucleus]].  (2) [[Biology:Homologous chromosome|Homologous chromosome]]s originating from different cells (i.e. non-sister chromosomes) align in pairs and undergo [[Biology:Homologous recombination|recombination]] involving double-strand break repair.  (3) Two successive [[Biology:Cell division|cell division]]s (without duplication of chromosomes) result in haploid gametes that can then repeat the meiotic cycle. During step (2), damages in DNA of the [[Biology:Germline|germline]] can be removed by double-strand break repair.<ref name = Bernstein1987>Bernstein H, Hopf FA, Michod RE. The molecular basis of the evolution of sex. Adv Genet. 1987;24:323-70. doi: 10.1016/s0065-2660(08)60012-7. PMID: 3324702</ref>  In particular, double-strand breaks in one duplex DNA molecule can be accurately repaired using information from a homologous intact DNA molecule by the process of [[Biology:Homologous recombination|homologous recombination]].<ref name = Bernstein1987/>

== Defective DSB repair ==
Although there is no universal model to explain disease etiology caused by DNA repair deficiency, it is said that the accumulation of unrepaired DNA damage may lead to various diseases, including various metabolic syndromes and types of [[Medicine:Cancer|cancer]]s.<ref>{{cite journal | vauthors = Tiwari V, Wilson DM | title = DNA Damage and Associated DNA Repair Defects in Disease and Premature Aging | journal = American Journal of Human Genetics | volume = 105 | issue = 2 | pages = 237–257 | date = August 2019 | pmid = 31374202 | pmc = 6693886 | doi = 10.1016/j.ajhg.2019.06.005 }}</ref><ref>{{cite journal | vauthors = Mercer JR, Cheng KK, Figg N, Gorenne I, Mahmoudi M, Griffin J, Vidal-Puig A, Logan A, Murphy MP, Bennett M | display-authors = 6 | title = DNA damage links mitochondrial dysfunction to atherosclerosis and the metabolic syndrome | journal = Circulation Research | volume = 107 | issue = 8 | pages = 1021–1031 | date = October 2010 | pmid = 20705925 | pmc = 2982998 | doi = 10.1161/CIRCRESAHA.110.218966 }}</ref> Some examples of diseases caused by defects of DSB repair mechanisms are listed below: 
*[[Medicine:Fanconi anemia|Fanconi Anemia]] (FA) and [[Medicine:Hereditary breast–ovarian cancer syndrome|Hereditary breast and ovarian cancer]] (HBOC) syndrome are caused by defects in homologous recombination.<ref name=":6">{{cite journal | vauthors = Katsuki Y, Takata M | title = Defects in homologous recombination repair behind the human diseases: FA and HBOC | language = en-US | journal = Endocrine-Related Cancer | volume = 23 | issue = 10 | pages = T19–T37 | date = October 2016 | pmid = 27550963 | doi = 10.1530/ERC-16-0221 | doi-access = free }}</ref> Biallelic mutation of either BRCA1/2 gene results in the loss of homologous recombination activity.<ref name=":6" />
* Chordomas, a rare bone tumour, might suggest defects in homologous recombination and mutations affecting HR-related genes.<ref>{{cite journal | vauthors = Gröschel S, Hübschmann D, Raimondi F, Horak P, Warsow G, Fröhlich M, Klink B, Gieldon L, Hutter B, Kleinheinz K, Bonekamp D, Marschal O, Chudasama P, Mika J, Groth M, Uhrig S, Krämer S, Heining C, Heilig CE, Richter D, Reisinger E, Pfütze K, Eils R, Wolf S, von Kalle C, Brandts C, Scholl C, Weichert W, Richter S, Bauer S, Penzel R, Schröck E, Stenzinger A, Schlenk RF, Brors B, Russell RB, Glimm H, Schlesner M, Fröhling S | display-authors = 6 | title = Defective homologous recombination DNA repair as therapeutic target in advanced chordoma | journal = Nature Communications | volume = 10 | issue = 1 | pages = 1635 | date = April 2019 | pmid = 30967556 | doi = 10.1038/s41467-019-09633-9 | pmc = 6456501 | bibcode = 2019NatCo..10.1635G }}</ref> 
* Defects in the NHEJ mechanism are related to the mutations in hRAD50 and/or hMRE11 genes in mismatch repair deficient tumors.<ref>{{cite journal | vauthors = Koh KH, Kang HJ, Li LS, Kim NG, You KT, Yang E, Kim H, Kim HJ, Yun CO, Kim KS, Kim H | display-authors = 6 | title = Impaired nonhomologous end-joining in mismatch repair-deficient colon carcinomas | journal = Laboratory Investigation; A Journal of Technical Methods and Pathology | volume = 85 | issue = 9 | pages = 1130–1138 | date = September 2005 | pmid = 16025146 | doi = 10.1038/labinvest.3700315 | s2cid = 21197331 | doi-access = free }}</ref>

== See also ==
* [[Biology:DNA repair|DNA damage & repair]]
* [[Biology:Homologous recombination|Homologous Recombination]]
* [[Biology:Synthesis-dependent strand annealing|Synthesis-dependent strain annealing]]
* [[Biology:Non-homologous end joining|Non-homologous end joining]]
* [[Biology:Microhomology-mediated end joining|Microhomology-mediated end joining]] 
* [[Biology:Cell cycle|Cell cycle]]
* [[Biology:DNA synthesis|DNA synthesis]]

== References ==
{{Reflist}}

[[Category:DNA repair]]

{{Sourceattribution|Double-strand break repair model}}