Evidence that localised variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair Export

@article{citeulike:6082942, abstract = {Understanding the origins of localised 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 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 [\~{}] 1800 primate promoters were 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 [\~{}] 50\% of the variance in substitution rate accounted for. Using signal processing techniques, a dominant oscillation at [\~{}] 200 bp was evident in both the substitution rate and nucleosome score. Our results support a role for differential DNA repair rates between open and closed chromatin in the spatial distribution of rate heterogeneity. 10.1093/molbev/msp253}, author = {Ying, Hua and Epps, Julian and Williams, Rohan and Huttley, Gavin}, citeulike-article-id = {6082942}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/molbev/msp253}, citeulike-linkout-1 = {http://mbe.oxfordjournals.org/content/msp253/.abstract}, citeulike-linkout-2 = {http://mbe.oxfordjournals.org/content/msp253/.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19843619}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19843619}, day = {20}, doi = {10.1093/molbev/msp253}, journal = {Mol Biol Evol}, keywords = {chromatin, genome\_architecture, nucleosome, primate}, month = {October}, pages = {msp253+}, posted-at = {2009-11-07 14:02:12}, priority = {2}, title = {Evidence that localised variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair}, url = {http://dx.doi.org/10.1093/molbev/msp253}, year = {2009} }

TY - JOUR ID - citeulike:6082942 L3 - citeulike-article-id:6082942 N2 - Understanding the origins of localised 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 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 [~] 1800 primate promoters were 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 [~] 50% of the variance in substitution rate accounted for. Using signal processing techniques, a dominant oscillation at [~] 200 bp was evident in both the substitution rate and nucleosome score. Our results support a role for differential DNA repair rates between open and closed chromatin in the spatial distribution of rate heterogeneity. 10.1093/molbev/msp253 JF - Mol Biol Evol TI - Evidence that localised variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair SP - msp253 KW - chromatin KW - genome_architecture KW - nucleosome KW - primate AU - Ying, Hua AU - Epps, Julian AU - Williams, Rohan AU - Huttley, Gavin PY - 2009/10/20/ UR - http://dx.doi.org/10.1093/molbev/msp253 ER -