Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs

Auton, Adam; Li, Ying Rui; Kidd, Jeffrey M.; Oliveira, Kyle C.; Nadel, Julie; Holloway, J. Kim; Hayward, Jessica J.; Cohen, Paula E.; Greally, John M.; Wang, Jun; Bustamante, Carlos D.; Boyko, Adam R.

doi:10.1371/journal.pgen.1003984

Cited by 225 publications

(289 citation statements)

References 34 publications

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“…On the contrary, recombination is essentially universal. In canids where PRDM9 is absent, recombination occurs in CpG-rich regions around promoters with little association with H3K4me3 marks (Auton et al 2013). In mouse prdm9 mutants, recombination hotspots are reverted to gene promoters as it is observed in yeast, plants, and in our analysis, suggesting a functional gain to specify location of recombination (Brick et al 2012).…”

Section: Te-related Motifs Are Thus Present In Recombinogenic Windowssupporting

confidence: 60%

“…These two different categories (specific TE-associated motif and simple repeats) were found in previous analyses in other species (Comeron et al 2012;Auton et al 2013;Choi et al 2013;Wijnker et al 2013;Shilo et al 2015). The A-stretch motif was already found in Arabidopsis, human, and Drosophila to be associated with recombination in 2-kb areas around CO events, suggesting that A-stretches do not directly induce recombination but that they contribute to its occurrence as a result of DNA decompaction (Myers et al 2008;Comeron et al 2012;Shilo et al 2015).…”

Section: Te-related Motifs Are Thus Present In Recombinogenic Windowssupporting

confidence: 56%

“…The second motif found in wheat is CCG that could be related to CCN found in canids, Arabidopsis, and Drosophila (Comeron et al 2012;Auton et al 2013;Shilo et al 2015). Our complete motif was CCGCCGNCGCCGCCGCCGCC.…”

Section: Te-related Motifs Are Thus Present In Recombinogenic Windowsmentioning

confidence: 69%

“…Previous studies in Arabidopsis, Drosophila, and dogs discovered recombination-associated motifs like A-stretch motif, CCT, CCN repeats, and CpG (Comeron et al 2012;Auton et al 2013;Wijnker et al 2013;Shilo et al 2015;Choi et al 2016). To evaluate the existence of recombinationassociated motifs in wheat, we searched for DNA motifs overrepresented in Rec intervals without a priori using MEME Suite and the base frequency of the chromosome (see Materials and Methods for details).…”

Section: Recombinogenic Regions Have Different Composition In Tes Andmentioning

confidence: 99%

“…It seems to be very specific to a few species and is rather rare among eukaryotes. PRDM9 is absent in plants (Zhang and Ma 2012), birds (Muñoz-Fuentes et al 2011), Drosophila (Heil and Noor 2012), and even in some mammals such as the canids (Muñoz-Fuentes et al 2011;Auton et al 2013). On the contrary, recombination is essentially universal.…”

Section: Te-related Motifs Are Thus Present In Recombinogenic Windowsmentioning

confidence: 99%

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High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

et al. 2017

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During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry 60-70% of the genes. Identifying sequence and/or chromosome features affecting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed fine-scale mapping of COs and revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length. We used 774 SNPs to genotype 180 varieties representative of the Asian and European genetic pools and a segregating population of 1270 F 6 lines. We observed a common location for ancestral COs (predicted through linkage disequilibrium) and the COs derived from the segregating population. We delineated 73 small intervals (,26 kb) on chromosome 3B that contained 252 COs. We observed a significant association of COs with genic features (73 and 54% in recombinant and nonrecombinant intervals, respectively) and with those expressed during meiosis (67% in recombinant intervals and 48% in nonrecombinant intervals). Moreover, while the recombinant intervals contained similar amounts of retrotransposons and DNA transposons (42 and 53%), nonrecombinant intervals had a higher level of retrotransposons (63%) and lower levels of DNA transposons (28%). Consistent with this, we observed a higher frequency of a DNA motif specific to the TIR-Mariner DNA transposon in recombinant intervals. KEYWORDS recombination; meiosis; bread wheat; linkage disequilibrium; transposon; hotspot; sequence motif M EIOTIC recombination is a process that allows reshuffling of diversity by the reciprocal exchange of DNA called a crossover (CO). This phenomenon is conserved in most eukaryotes (for a review see Mercier et al. 2015) and follows the formation of a double-strand break (DSB) of DNA generated by the topoisomerase SPO11 complex. However, the number of DSBs is at least 10-to 50-fold greater than the number of COs which rarely exceeds three per bivalent chromosome per meiosis (Mercier et al. 2015). This paucity of COs per meiosis with regards to the number of DSBs suggests the existence of a tight control and regulation of recombination in plants that promote DSB repair in a manner that does not lead to COs. For example, the study of the two helicases AtFANCM and RECQ4 (AtRECQ4A and AtRECQ4B) (Crismani et al. 2012;Knoll et al. 2012;Girard et al. 2014;Séguéla-Arnaud et al. 2015) revealed three-and sixfold CO frequency increases in the Atfancm single mutant and the Atrecq4a/Atrecq4b double mutant, respectively, compared to the wild type. These increases result from additional COs from the class-II pathway which suggests that FANCM and RECQ4 prevent CO formation and direct recombination intermediates towar...

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Section: Te-related Motifs Are Thus Present In Recombinogenic Windowssupporting

confidence: 60%

Section: Te-related Motifs Are Thus Present In Recombinogenic Windowssupporting

confidence: 56%

Section: Te-related Motifs Are Thus Present In Recombinogenic Windowsmentioning

confidence: 69%

Section: Recombinogenic Regions Have Different Composition In Tes Andmentioning

confidence: 99%

Section: Te-related Motifs Are Thus Present In Recombinogenic Windowsmentioning

confidence: 99%

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High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

et al. 2017

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Unraveling recombination rate evolution using ancestral recombination maps

2014

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Recombination maps of ancestral species can be constructed from comparative analyses of genomes from closely related species, exemplified by a recently published map of the human-chimpanzee ancestor. Such maps resolve differences in recombination rate between species into changes along individual branches in the speciation tree, and allow identification of associated changes in the genomic sequences. We describe how coalescent hidden Markov models are able to call individual recombination events in ancestral species through inference of incomplete lineage sorting along a genomic alignment. In the great apes, speciation events are sufficiently close in time that a map can be inferred for the ancestral species at each internal branch - allowing evolution of recombination rate to be tracked over evolutionary time scales from speciation event to speciation event. We see this approach as a way of characterizing the evolution of recombination rate and the genomic properties that influence it.

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GC‐biased gene conversion links the recombination landscape and demography to genomic base composition

Mugal

Weber²,

Ellegren

2015

BioEssays

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The origin and evolutionary dynamics of the spatial heterogeneity in genomic base composition have been debated since its discovery in the 1970s. With the recent availability of numerous genome sequences from a wide range of species it has been possible to address this question from a comparative perspective, and similarities and differences in base composition between groups of organisms are becoming evident. Ample evidence suggests that the contrasting dynamics of base composition are driven by GC-biased gene conversion (gBGC), a process that is associated with meiotic recombination. In line with this hypothesis, base composition is associated with the rate of recombination and the evolutionary dynamics of the recombination landscape, therefore, governs base composition. In addition, and at first sight perhaps surprisingly, the relationship between demography and genomic base composition is in agreement with the gBGC hypothesis: organisms with larger populations have higher GC content than those with smaller populations.

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Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs

Cited by 225 publications

References 34 publications

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

Unraveling recombination rate evolution using ancestral recombination maps

GC‐biased gene conversion links the recombination landscape and demography to genomic base composition

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