Intense and highly localized gene conversion activity in human meiotic crossover hot spots

Abstract

Meiotic gene conversion has an important role in allele diversification and in the homogenization of gene and other repeat DNA sequence families 1-5 , sometimes with pathological consequences 6,7 . But little is known about the dynamics of gene conversion in humans and its relationship to meiotic crossover. We therefore developed screening and selection methods to characterize sperm conversions in two meiotic crossover hot spots in the major histocompatibility complex (MHC) 8 and one in the sex chromosomal pseudoautosomal pairing region PAR1 (ref. 9). All three hot spots are active in gene conversion and crossover. Conversion tracts are short and define a steep bidirectional gradient centered at the peak of crossover activity, consistent with crossovers and conversions being produced by the same recombination-initiating events. These initiations seem to be spread over a narrow zone, rather than occurring at a single site, and seem preferentially to yield conversions rather than crossovers. Crossover breakpoints are more broadly diffused than conversion breakpoints, suggesting either differences between conversion and crossover processing after initiation or the existence of a quality control checkpoint at which short interactions between homologous chromosomes are preferentially aborted as conversions.Meiotic gene conversion in humans is defined as the recombinational transfer of information between alleles or loci without crossover. (This definition, though widely used, is not necessarily congruent with conversion classically defined by non-2:2 meiotic segregation ratios and does not include crossovers accompanied by conversion.) Homogenization events in multigene and dispersed repeat sequence families and in palindromic DNA 3-5 , as well as the direct detection of de novo conversion events in families 6,10 and in sperm 11,12 , provide extensive evidence for interlocus conversion. Indirect evidence for interallelic conversion comes from seemingly anomalous low levels of linkage disequilibrium seen between some closely linked markers 13 and from patchwork patterns of allelic diversity 14,15 (though such patchworks could arise from sequential crossovers). Sperm analysis at the HLA-DPB1 locus has provided direct evidence that true interallelic conversions do occur, though at low frequency 16 . The relationship between crossover and conversion in humans, however, is unclear.The high-resolution definition of human crossover hot spots by sperm typing 8,9,15 has allowed us to investigate the connection between crossover and interallelic conversion without crossover. We chose the hot spot DNA3 located in the MHC for analysis 8 , because of its intense crossover activity and the availability of sperm donors with multiple single nucleotide polymorphism (SNP) heterozygosities needed to monitor recombination events. Our initial approach was similar to that used to detect conversion in HLA-DPB1 (ref. 16; Fig. 1a). We amplified pools of sperm DNA by PCR using allele-specific primers outside the hot spot to amplify one haplo...

Regulating double-stranded DNA break repair towards crossover or non-crossover during mammalian meiosis

“…Whereas the size of gene conversion tracts among CO products was found to be around 500 bp (see above), among NCO the conversion tracts are considerably shorter, with a mean length estimated between 50 and 300 bp (Jeffreys & May 2004, Guillon et al 2005. This is consistent with the fact that NCO and CO are outcomes of different DSB repair pathways, involving different recombination intermediates.…”

“…Several aspects of NCO formation have been compared with CO. NCO are clustered at the center of CO hotspots, with a sharp decrease in gene conversion frequencies on both sides, indicating that both CO and NCO are the products of initiation events taking place in the same region (Jeffreys & May 2004, Guillon et al 2005. NCO products are formed with a kinetics similar to those of CO, from middle to late pachynema (Guillon et al 2005).…”

“…Most of the data comes from molecular analysis at a few specific CO hotspots in the human and mouse genomes. These studies have shown that most CO hotspots are also NCO hotspots, indicating that the same initiating regions can lead to both CO and NCO products (Guillon & de Massy 2002, Jeffreys & May 2004.…”

Sequence analysis of the mannose-binding lectin (MBL2) gene reveals a high degree of heterozygosity with evidence of selection

“…Several studies demonstrate that, at intragenic distance, gene conversion without exchange of flanking markers, rather than crossing over, is likely to interrupt the LD structure. [85][86][87] In MBL2, gene conversion could act as a second-level mutator between haplotypes. For the human major histocompatibility complex class I and class II loci, gene conversion is involved in the generation and maintenance of polymorphism in the sequence encoding the peptide-binding region by some form of balancing selection, most probably over dominant selection.…”

No effect of recombination on the efficacy of natural selection in primates

“…However, while a cross-over anywhere between two sites will decrease the association, a gene conversion event will only do so if the conversion track (on the order of ∼100 bp) overlaps one of the two sites. Thus, even if the per base pair rate of gene conversion is several fold higher than crossing-over (Jeffreys and May 2004), the allelic association between sites that are more than a couple of hundred base pairs apart will primarily be broken down by crossing-over (Przeworski and Wall 2001). In other words, crossing-over should be the primary determinant of the strength of HRI, unless the cross-over rate is very low (or the sites are very close).…”