Evolutionary rates are not constant across the human genome but genes in …

• Abstract
• Background
• Results and Discussion
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Biology Articles » Evolutionary Biology » Chromatin structure and evolution in the human genome » Figures

Figures

- Chromatin structure and evolution in the human genome

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Figure 1 Increased mutation rates in closed chromatin at non-CpG sites. (A+B) Mean intergenic and ancient repeat divergence observed across chromatin categories (Intergenic r²: = 0.87, p = 9.1e-05; Intergenic repeats only r²: = 0.93, p = 7.3e-06; Ancient repeats only r²: = 0.93, p = 6.1e-06). (C) Intergenic divergence of each 1 Mb clone from chromosome 1 against their corresponding chromatin score (10 clones containing less than 10,000 intergenic bases were excluded). (D) Mean human SNP densities (SNPs/bp) observed across chromatin categories (All SNPs r²: = 0.89, p = 0.016; Single random detection protocol (TSCM0019) SNPs only r²: = 0.93, p = 0.008).

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Figure 2 Comparison of splice site divergence observed across chromatin categories. (A) The divergence at non-CpG fourfold degenerate and intronic sites on autosomes only, with the divergence observed across the splice sites of the most closed (B) and open (C) genes shown below. (Closed exonic vs. closed intronic Mann-Whitney U test: p = 4.4e-16; open exonic vs. open intronic Mann-Whitney U-test: p = 0.053)

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Figure 3 The distribution of gene expression profiles and CpG island genes across chromatin categories. (A) The mean chromatin structure (log2(Open:Input)) of genes of differing expression breadth across normal tissues (Kruskal-Wallis p = 7.5e-6) (B) The percentage of genes across chromatin categories that are associated with a CpG island.

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Figure 4 Human-mouse divergence across chromatin categories. Mean dN (A), dN/dS (B) and dS (C) in human/mouse coding sequence alignments. (All protein coding genes dS r²: = 0.99, p = 0.001; dN r²: = 0.92, p = 0.01; dN/dS r²: = 0.92, p = 0.009. Genes associated with a CpG island dS r²: = 0.72, p = 0.07; dN r²: = 0.17, p = 0.5; dN/dS r²: = 0.64, p = 0.1. Genes not associated with a CpG island only dS r²: = 0.84, p = 0.03; dN r²: = 0.95, p = 0.005; dN/dS r²: = 0.92, p = 0.01.).

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Figure 5 The effect of ESEs on fourfold degenerate site divergence and the ncRNA gene distributions observed across chromatin categories. (A+B) The observed rate of transitions and transversions respectively, at fourfold degenerate sites with and without ESE sites excluded (Fourfold degenerate site transversions r²: = 0.02, p = 0.69; fourfold degenerate site transversions at non-ESE sites r²: = 0.13, p = 0.30; intergenic transversions r²: = 0.92, p = 1.2e-05. Fourfold degenerate site transitions r²: = 0.78, p = 0.001; fourfold degenerate site transitions at non-ESE sites r²: = 0.67, p = 0.004; intergenic transitions r²: = 0.81, p = 4.0e-04). (C+D) The percentage of genes in each chromatin category that are of each Ensembl ncRNA class. Only the distributions of rRNAs and snRNAs show a significant negative correlation with chromatin structure (rRNA r²: = 0.96, p = 0.004; snRNA r²: = 0.92, p = 0.01)

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