Why Is the Centromere So Cold?

Choo, K.H. Andy

doi:10.1101/gr.8.2.81

Cited by 92 publications

(82 citation statements)

References 22 publications

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“…In all organisms, these rates vary a lot with in particular a frequent strong suppression effect in and near the centromeres and typically enhancements near the telomeres ( Jones 1984;Mezard 2006). Many forces shape these variations: (1) the distribution of chiasma precursors, which may be approached by counting early recombination nodules; (2) chromatin compaction, leading in particular to the centromere effect (Choo 1998);and (3) factors that may determine the way precursors commit or not to turn into COs, including the forces behind interference and obligate chiasma effects. In the case of mouse chromosomes, where the centromere is at one end and the telomere at the other end, this second force may explain the strong asymmetry observed in the experimental curves of Figures 3 and 7.…”

Section: 34mentioning

confidence: 99%

“…In all cases, CO density is not uniformly distributed along physical chromosomes; the 1 pattern varies greatly among species and even among chromosomes within a species. A very common rule is that COs are strongly suppressed at the centromere regions, even if in some species COs have been found preferentially localized in pericentromeric regions ( Jones 1984;Choo 1998; see review by Mezard 2006). Although the causes of such variability are still not understood, it is clear that CO distribution is a highly regulated process.…”

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confidence: 99%

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Patterns of Recombination and MLH1 Foci Density Along Mouse Chromosomes: Modeling Effects of Interference and Obligate Chiasma

et al. 2007

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Crossover interference in meiosis is often modeled via stationary renewal processes. Here we consider a new model to incorporate the known biological feature of ''obligate chiasma'' whereby in most organisms each bivalent almost always has at least one crossover. The initial crossover is modeled as uniformly distributed along the chromosome, and starting from its position, subsequent crossovers are placed with forward and backward stationary renewal processes using a chi-square distribution of intercrossover distances. We used our model as well as the standard chi-square model to simulate the patterns of crossover densities along bivalents or chromatids for those having zero, one, two, or three or more crossovers; indeed, such patterns depend on the number of crossovers. With both models, simulated patterns compare very well to those found experimentally in mice, both for MLH1 foci on bivalents and for crossovers on genetic maps. However, our model provides a better fit to experimental data as compared to the standard chi-square model, particularly regarding the distribution of numbers of crossovers per chromosome. Finally, our model predicts an enhancement of the recombination rate near the extremities, which, however, explains only a part of the pattern observed in mouse.

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Section: 34mentioning

confidence: 99%

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confidence: 99%

Patterns of Recombination and MLH1 Foci Density Along Mouse Chromosomes: Modeling Effects of Interference and Obligate Chiasma

et al. 2007

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“…This nonhomogeneity of CO distribution is the basis of the definition of recombination hotspots and coldspots (which have significantly high and low CO frequencies, respectively). A general rule is that centromeres are cold regions (Choo 1998) with a few exceptions such as Welsh onion where COs cluster close to centromeres (Jones 1984).…”

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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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“…Apart from work in Drosophila, however, DNA sequence diversity has rarely been studied for loci in such regions. Many species have chromosomal regions with low crossing over surrounding the centromeres (Choo 1997(Choo , 1998, including the plants maize and Solanum/Lycopersicon (Sherman and Stack 1995;Anderson et al 2003). Previous studies of the relationship between diversity and recombination rates in the plants Lycopersicon (Baudry et al 2001) and maize (Tenaillon et al 2002) did not include loci in very low recombination regions near centromeres (and did not find clear evidence for a correlation between nucleotide diversity and estimated recombination rates).…”

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High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata

et al. 2008

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Differences in neutral diversity at different loci are predicted to arise due to differences in mutation rates and from the ''hitchhiking'' effects of natural selection. Consistent with hitchhiking models, Drosophila melanogaster chromosome regions with very low recombination have unusually low nucleotide diversity. We compared levels of diversity from five pericentromeric regions with regions of normal recombination in Arabidopsis lyrata, an outcrossing close relative of the highly selfing A. thaliana. In contrast with the accepted theoretical prediction, and the pattern in Drosophila, we found generally high diversity in pericentromeric genes, which is consistent with the observation in A. thaliana. Our data rule out balancing selection in the pericentromeric regions, suggesting that hitchhiking is more strongly reducing diversity in the chromosome arms than the pericentromere regions.

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Why Is the Centromere So Cold?

Cited by 92 publications

References 22 publications

Patterns of Recombination and MLH1 Foci Density Along Mouse Chromosomes: Modeling Effects of Interference and Obligate Chiasma

Patterns of Recombination and MLH1 Foci Density Along Mouse Chromosomes: Modeling Effects of Interference and Obligate Chiasma

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

High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata

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