Crossovers are associated with mutation and biased gene conversion at recombination hotspots

Abstract

Meiosis is a potentially important source of germline mutations, as sites of meiotic recombination experience recurrent double-strand breaks (DSBs). However, evidence for a local mutagenic effect of recombination from population sequence data has been equivocal, likely because mutation is only one of several forces shaping sequence variation. By sequencing large numbers of single crossover molecules obtained from human sperm for two recombination hotspots, we find direct evidence that recombination is mutagenic: Crossovers carry more de novo mutations than nonrecombinant DNA molecules analyzed for the same donors and hotspots. The observed mutations were primarily CG to TA transitions, with a higher frequency of transitions at CpG than non-CpGs sites. This enrichment of mutations at CpG sites at hotspots could predominate in methylated regions involving frequent single-stranded DNA processing as part of DSB repair. In addition, our data set provides evidence that GC alleles are preferentially transmitted during crossing over, opposing mutation, and shows that GC-biased gene conversion (gBGC) predominates over mutation in the sequence evolution of hotspots. These findings are consistent with the idea that gBGC could be an adaptation to counteract the mutational load of recombination. meiotic recombination | crossover | sequence evolution | biased gene conversion | mutation M eiotic recombination, localized in recombination hotspots, not only increases genetic diversity via the formation of new haplotypes but is also an important driver of sequence evolution. The binding sites used by the human recombination machinery involving PRDM9 (PR domain containing 9) are more eroded in humans than the same sequences in chimps, given that PRDM9 in chimps uses different binding sites (1). Moreover, regions in close vicinity to these PRDM9 binding sites also showed a significant enrichment of polymorphisms in humans (2). In addition, within-and between-species sequence diversity positively correlates with regions of high recombination activity in humans (3-7) and other eukaryotes (reviewed in refs. 8-10).One process recognized as a major evolutionary force reshaping the genomic nucleotide landscape at recombination hotspots, as shown in humans (6), chimpanzees (6, 11), mice (12), yeast (13), and metazoans (14), is GC-biased gene conversion (gBGC). In gBGC, the repair of heteroduplex tracts formed during meiotic recombination leads to the nonMendelian segregation of alleles favoring GC over AT variants. The precise molecular mechanisms leading to gBGC have yet to be unraveled, but experimental evidence has shown that in crossovers (COs) of fission yeast, GC alleles can be overtransmitted within ∼1-2 kb in length of the double-strand break (DSB) region (13), implicating mismatch repair (15).However, it is also plausible that the higher sequence variation observed at recombination hotspots is a result of a mutagenic effect of recombination: meiotic recombination is initiated by DSBs, which are associated with an increased mutati...

Local and sex-specific biases in crossover vs. noncrossover outcomes at meiotic recombination hot spots in mice

“…Gene conversion is biased in favor of transmission of GC alleles in many eukaryotes (Duret and Galtier 2009). Such a bias has been observed directly in noncrossover (Odenthal-Hesse et al 2014) and crossover (Arbeithuber et al 2015) recombination products in human sperm and can explain patterns of GC content enrichment at mouse hot spots (Clement and Arndt 2013). Accordingly, we found that, in males, noncrossovers frequently showed significant bias, resulting in more conversion to GC than to AT (Supplemental Table S2).…”

Meiotic Recombination: The Essence of Heredity

“…Moreover, direct interaction between Rev1, Polz, and components of the DSB-forming machinery (Spo11, Mei4, Rec114) is suggested by yeast twohybrid interactions (Arbel-Eden et al 2013). Further support for a role of TLS polymerases in meiosis comes from the observation that Polz also makes a major contribution to the elevated mutation rate that is associated with meiotic recombination (Arbeithuber et al 2015;Rattray et al 2015). Recruitment of alternative DNA polymerases to damage sites is mediated by ubiquitylation of PCNA at K164 (Dieckman et al 2012).…”

Quantification of GC-biased gene conversion in the human genome

“…Direct observations of gBGC have been first provided by the analysis of a few specific recombination hotspots (OdenthalHesse et al 2014;Arbeithuber et al 2015). Recently, Williams and colleagues published a large-scale study of gene conversion tracts associated with noncrossover (NCO) recombination events in humans (Williams et al 2015).…”