ArticleMolecular biology and evolution2010
Evidence that localized variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair.
Article in Molecular biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Predicting regional somatic mutation rates using DNA motifs.PLoS computational biology · 2023Article
- Chromatin structure influences rate and spectrum of spontaneous mutations inGenome research · 2023Article
- Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders.Frontiers in neuroscience · 2023Article
- Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome.Nucleic acids research · 2021Article
- Quantifying Influences on Intragenomic Mutation Rate.G3 (Bethesda, Md.) · 2020Article
- [Identification of nucleosome positioning using support vector machine method based on comprehensive DNA sequence feature].Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi · 2020Article
- Article
- Evidence of selection for an accessible nucleosomal array in human.BMC genomics · 2016Article
- The effects of chromatin organization on variation in mutation rates in the genome.Nature reviews. Genetics · 2015Review
- Article
- Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition.Genome research · 2014Article
- Properties and rates of germline mutations in humans.Trends in genetics : TIG · 2013Review
- Segmenting the human genome based on states of neutral genetic divergence.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.Genome research · 2013Article
- Conserved substitution patterns around nucleosome footprints in eukaryotes and Archaea derive from frequent nucleosome repositioning through evolution.PLoS computational biology · 2013Article
- Nucleoid-associated proteins affect mutation dynamics in E. coli in a growth phase-specific manner.PLoS computational biology · 2012Article
- Widespread signatures of recent selection linked to nucleosome positioning in the human lineage.Genome research · 2011Article
- Variation in the mutation rate across mammalian genomes.Nature reviews. Genetics · 2011Review
- Review
- Evidence for a high mutation rate at rapidly evolving yeast centromeres.BMC evolutionary biology · 2011Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the origins of localized substitution rate heterogeneity has important implications for identifying functional genomic sequences. Outside of gene regions, the origins of rate heterogeneity remain unclear. Experimental studies establish that chromatin compaction affects rates of both DNA lesion formation and repair. A functional association between chromatin status and 5-methyl-cytosine also exists. These suggest that both the total rate and the type of substitution will be affected by chromatin status. Regular positioning of nucleosomes, the building block of chromatin, further predicts that substitution rate and type should vary spatially in an oscillating manner. We addressed chromatin's influence on substitution rate and type in primates. Matched numbers of sites were sampled from Dnase I hypersensitive (DHS) and closed chromatin control flank (Flank). Likelihood ratio tests revealed significant excesses of total and of transition substitutions in Flank compared with matched DHS for both intergenic and intronic samples. An additional excess of CpG transitions was evident for the intergenic, but not intronic, regions. Fluctuation in substitution rate along approximately 1,800 primate promoters was measured using phylogenetic footprinting. Significant positive correlations were evident between the substitution rate and a nucleosome score from resting human T-cells, with up to approximately 50% of the variance in substitution rate accounted for. Using signal processing techniques, a dominant oscillation at approximately 200 bp was evident in both the substitution rate and the nucleosome score. Our results support a role for differential DNA repair rates between open and closed chromatin in the spatial distribution of rate heterogeneity.
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