Editing Chromosomal crossover (section)

== Biochemistry of meiotic recombination ==
[[File:Homologous Recombination.jpg|thumb|upright=1.35|A current model of meiotic recombination, initiated by a double-strand break or gap, followed by pairing with a homologous chromosome and strand invasion to initiate the recombinational repair process. Repair of the gap can lead to crossover (CO) or non-crossover (NCO) of the flanking regions. CO recombination is thought to occur by the Double Holliday Junction (DHJ) model, illustrated on the right, above. NCO recombinants are thought to occur primarily by the Synthesis Dependent Strand Annealing (SDSA) model, illustrated on the left, above. Most recombination events appear to be the SDSA type.]]

Meiotic recombination may be initiated by double-stranded breaks that are introduced into the DNA by exposure to DNA damaging agents,<ref name="ReferenceA"/> or the [[Spo11]] protein.<ref>{{cite journal | vauthors = Keeney S, Giroux CN, Kleckner N | title = Meiosis-specific DNA double-strand breaks are catalyzed by Spo11, a member of a widely conserved protein family | journal = Cell | volume = 88 | issue = 3 | pages = 375–384 | date = February 1997 | pmid = 9039264 | doi = 10.1016/S0092-8674(00)81876-0 | s2cid = 8294596 | doi-access = free }}</ref> One or more [[exonuclease]]s then digest the [[Directionality (molecular biology)|5' ends]] generated by the double-stranded breaks to produce 3' single-stranded DNA tails (see diagram). The meiosis-specific [[recombinase]] [[Dmc1]] and the general recombinase [[Rad51]] coat the single-stranded DNA to form nucleoprotein filaments.<ref>{{cite journal | vauthors = Sauvageau S, Stasiak AZ, Banville I, Ploquin M, Stasiak A, Masson JY | title = Fission yeast rad51 and dmc1, two efficient DNA recombinases forming helical nucleoprotein filaments | journal = Molecular and Cellular Biology | volume = 25 | issue = 11 | pages = 4377–4387 | date = June 2005 | pmid = 15899844 | pmc = 1140613 | doi = 10.1128/MCB.25.11.4377-4387.2005 }}</ref> 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, which subsequently anneals to the single-stranded DNA generated from the other end of the initial double-stranded break. 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 (genetics)|chiasma]]''. The Holliday junction is a [[Tetrahedron|tetrahedral]] structure which can be 'pulled' by other recombinases, moving it along the four-stranded structure.{{cn|date=December 2024}}
{{gallery |mode=packed
|width=160 |height=160
|Image:Holliday Junction.svg|Holliday Junction
|Image:Holliday junction.jpg|Molecular structure of a Holliday junction.
|Image:Holliday junction coloured.png|Molecular structure of a Holliday junction. From {{PDB|3CRX}}.
}}

===MSH4 and MSH5===
The MSH4 and MSH5 proteins form a hetero-oligomeric structure ([[Protein dimer|heterodimer]]) in yeast and humans.<ref name=Pochart>{{cite journal | vauthors = Pochart P, Woltering D, Hollingsworth NM | title = Conserved properties between functionally distinct MutS homologs in yeast | journal = The Journal of Biological Chemistry | volume = 272 | issue = 48 | pages = 30345–30349 | date = November 1997 | pmid = 9374523 | doi = 10.1074/jbc.272.48.30345 | doi-access = free }}</ref><ref name="pmid9787078">{{cite journal | vauthors = Winand NJ, Panzer JA, Kolodner RD | title = Cloning and characterization of the human and Caenorhabditis elegans homologs of the Saccharomyces cerevisiae MSH5 gene | journal = Genomics | volume = 53 | issue = 1 | pages = 69–80 | date = October 1998 | pmid = 9787078 | doi = 10.1006/geno.1998.5447 | doi-access = free }}</ref><ref name="pmid10029069">{{cite journal | vauthors = Bocker T, Barusevicius A, Snowden T, Rasio D, Guerrette S, Robbins D, Schmidt C, Burczak J, Croce CM, Copeland T, Kovatich AJ, Fishel R | display-authors = 6 | title = hMSH5: a human MutS homologue that forms a novel heterodimer with hMSH4 and is expressed during spermatogenesis | journal = Cancer Research | volume = 59 | issue = 4 | pages = 816–822 | date = February 1999 | pmid = 10029069 }}</ref>  In the yeast ''[[Saccharomyces cerevisiae]]'', MSH4 and MSH5 act specifically to facilitate crossovers between [[homologous chromosome]]s during [[meiosis]].<ref name=Pochart />  The MSH4/MSH5 complex binds and stabilizes double [[Holliday junction]]s and promotes their resolution into crossover products.  An MSH4 [[Muller's morphs#Hypomorph|hypomorphic]] (partially functional) mutant of ''S. cerevisiae'' showed a 30% genome-wide reduction in crossover numbers and a large number of [[Meiosis|meioses]] with non-exchange chromosomes.<ref name="pmid25467183">{{cite journal | vauthors = Krishnaprasad GN, Anand MT, Lin G, Tekkedil MM, Steinmetz LM, Nishant KT | title = Variation in crossover frequencies perturb crossover assurance without affecting meiotic chromosome segregation in Saccharomyces cerevisiae | journal = Genetics | volume = 199 | issue = 2 | pages = 399–412 | date = February 2015 | pmid = 25467183 | pmc = 4317650 | doi = 10.1534/genetics.114.172320 }}</ref>  Nevertheless, this [[mutant]] gave rise to [[spore]] viability patterns suggesting that [[Chromosome segregation|segregation]] of non-exchange chromosomes occurred efficiently.  Thus in ''S. cerevisiae'' proper segregation apparently does not entirely depend on crossovers between [[Homologous chromosome|homologous]] pairs.{{cn|date=December 2024}} In humans, biallelic loss of function variants to MSH4 and MSH5 are compatible with life, but are associated with azospermia in males (spermatogenic failure) and premature ovarian failure in females.<ref>{{cite web |url=https://www.omim.org/entry/602105 |title=Entry - *602105 - MutS HOMOLOG 4; MSH4 - OMIM }}</ref><ref>{{cite web |url=https://www.omim.org/entry/603382?search=msh5&highlight=msh5 | title=Entry - *603382 - MutS HOMOLOG 5; MSH5 - OMIM }}</ref>
[[File:Meiosis crossover.png|thumb|Chiasma is the point of crossing over of the arms of sister chromatids.  ]]

===Chiasma===
Chiasma (plural: chiasmata) are essential for the correct alignment and segregation of homologous chromosomes at meiosis I, and their frequency reflects the rate of genetic recombination, which contributes to variation among offspring. Chiasma number tends to increase with genome size, as larger genomes generally undergo more crossover events per meiosis.<ref>{{Cite journal |last=Ross-Ibarra |first=J. |date=March 2007 |title=Genome size and recombination in angiosperms: a second look |url=https://academic.oup.com/jeb/article/20/2/800-806/7324572 |journal=Journal of Evolutionary Biology |language=en |volume=20 |issue=2 |pages=800–806 |doi=10.1111/j.1420-9101.2006.01275.x |pmid=17305845 |issn=1010-061X}}</ref> Each homologous pair forms a [[Bivalent (genetics)|bivalent]] (or tetrad), consisting of four chromatids. The number and position of chiasmata influence the shape of bivalents, rod-shaped with one chiasma and ring-shaped with two or more.<ref>{{Cite journal |last1=López |first1=E. |last2=Pradillo |first2=M. |last3=Oliver |first3=C. |last4=Romero |first4=C. |last5=Cuñado |first5=N. |last6=Santos |first6=J. L. |date=January 2012 |title=Looking for natural variation in chiasma frequency in Arabidopsis thaliana |url=https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/err319 |journal=Journal of Experimental Botany |language=en |volume=63 |issue=2 |pages=887–894 |doi=10.1093/jxb/err319 |issn=1460-2431}}</ref><ref>{{Cite journal |last1=Zickler |first1=Denise |last2=Kleckner |first2=Nancy |date=2015-05-18 |title=Recombination, Pairing, and Synapsis of Homologs during Meiosis |url=https://doi.org/10.1101/cshperspect.a016626 |journal=Cold Spring Harbor Perspectives in Biology |volume=7 |issue=6 |pages=a016626 |doi=10.1101/cshperspect.a016626 |pmid=25986558 |issn=1943-0264|pmc=4448610 }}</ref> 

The grasshopper ''[[Melanoplus femurrubrum|Melanoplus femur-rubrum]]'' was exposed to an acute dose of [[X-ray]]s during each individual stage of [[meiosis]], and [[Chiasma (genetics)|chiasma]] frequency was measured.<ref name="pmid5797806">{{cite journal | vauthors = Church K, Wimber DE | title = Meiosis in the grasshopper: chiasma frequency after elevated temperature and x-rays | journal = Canadian Journal of Genetics and Cytology | volume = 11 | issue = 1 | pages = 209–216 | date = March 1969 | pmid = 5797806 | doi = 10.1139/g69-025 }}</ref>  Irradiation during the [[Leptotene stage|leptotene]]-[[Meiosis#zygotene|zygotene]] stages of [[meiosis]] (that is, prior to the [[Meiosis#Pachytene|pachytene]] period in which crossover recombination occurs) was found to increase subsequent chiasma frequency.  Similarly, in the grasshopper ''[[Chorthippus brunneus]]'', exposure to X-irradiation during the zygotene-early pachytene stages caused a significant increase in mean cell chiasma frequency.<ref name="pmid5289295">{{cite journal | vauthors = Westerman M | title = The effect of x-irradiation on chiasma frequency in Chorthippus brunneus | journal = Heredity | volume = 27 | issue = 1 | pages = 83–91 | date = August 1971 | pmid = 5289295 | doi = 10.1038/hdy.1971.73 | doi-access = free | bibcode = 1971Hered..27...83W }}</ref>  Chiasma frequency was scored at the later [[Meiosis#diplotene|diplotene-diakinesis]] stages of meiosis.  These results show that [[Ionizing radiation|ionising-radiation]] induced [[DNA repair|double-stranded DNA breaks]] were subsequently repaired by a crossover pathway leading to chiasma formation.<ref>{{Cite journal |last1=Szostak |first1=Jack W. |last2=Orr-Weaver |first2=Terry L. |last3=Rothstein |first3=Rodney J. |last4=Stahl |first4=Franklin W. |date=May 1983 |title=The double-strand-break repair model for recombination |url=https://linkinghub.elsevier.com/retrieve/pii/0092867483903318 |journal=Cell |language=en |volume=33 |issue=1 |pages=25–35 |doi=10.1016/0092-8674(83)90331-8}}</ref>

However, increased crossover frequency following radiation-induced DNA damage does not universally occur in all insects; for example, ''Drosophila'' females exhibit predominantly non-crossover repair pathways when responding to induced double-stranded DNA breaks, resulting in a relatively low ratio of crossovers to non-crossovers.<ref>{{Cite journal |last1=Mehrotra |first1=S. |last2=McKim |first2=K. S. |date=2006 |title=Temporal Analysis of Meiotic DNA Double-Strand Break Formation and Repair in Drosophila Females |journal=PLOS Genetics |language=en |volume=2 |issue=11 |pages=e200 |doi=10.1371/journal.pgen.0020200 |doi-access=free |issn=1553-7390 |pmc=1657055 |pmid=17166055}}</ref>

===Class I and class II crossovers===
Double-strand breaks are repaired by two pathways to generate crossovers in eukaryotes.<ref>{{cite journal | vauthors = Holloway JK, Booth J, Edelmann W, McGowan CH, Cohen PE | title = MUS81 generates a subset of MLH1-MLH3-independent crossovers in mammalian meiosis | journal = PLOS Genetics | volume = 4 | issue = 9 | pages = e1000186 | date = September 2008 | pmid = 18787696 | pmc = 2525838 | doi = 10.1371/journal.pgen.1000186 | doi-access = free }}</ref> The majority of them are repaired by MutL homologs MLH1 and MLH3, which defines the class I crossovers. The remaining are the result of the class II pathway, which is regulated by MUS81 endonuclease and [[FANCM]] translocase. There are interconnections between these two pathways—class I crossovers can compensate for the loss of class II pathway. In MUS81 knockout mice, class I crossovers are elevated, while total crossover counts at chiasmata are normal. However, the mechanisms underlining this crosstalk are not well understood. A recent study suggests that a scaffold protein called SLX4 may participate in this regulation.<ref>{{cite journal | vauthors = Holloway JK, Mohan S, Balmus G, Sun X, Modzelewski A, Borst PL, Freire R, Weiss RS, Cohen PE | display-authors = 6 | title = Mammalian BTBD12 (SLX4) protects against genomic instability during mammalian spermatogenesis | journal = PLOS Genetics | volume = 7 | issue = 6 | pages = e1002094 | date = June 2011 | pmid = 21655083 | pmc = 3107204 | doi = 10.1371/journal.pgen.1002094 | doi-access = free }}</ref> Specifically, SLX4 knockout mice largely phenocopies the MUS81 knockout—once again, an elevated class I crossovers while normal chiasmata count. In FANCM knockout mice, the class II pathway is hyperactivated, resulting in increased numbers of crossovers that are independent of the MLH1/MLH3 pathway.<ref>{{cite journal | vauthors = Tsui V, Lyu R, Novakovic S, Stringer JM, Dunleavy JE, Granger E, Semple T, Leichter A, Martelotto LG, Merriner DJ, Liu R, McNeill L, Zerafa N, Hoffmann ER, O'Bryan MK, Hutt K, Deans AJ, Heierhorst J, McCarthy DJ, Crismani W | display-authors = 6 | title = ''Fancm'' has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals | journal = Cell Genomics | volume = 3 | issue = 8 | pages = 100349 | date = August 2023 | pmid = 37601968 | pmc = 10435384 | doi = 10.1016/j.xgen.2023.100349 }}</ref>