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Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

Figure 2

Identification of species-specific differences in DHS sites.

Species-specific DHS sites were identified by edgeR (Materials and Methods). Boxplots show the distribution of number of reads per sample in 300 bp windows. For human DHS gains (a), the 3 human samples are all significantly more open than the other 2 species. Likewise, human DHS losses (b) show lower signal in human compared to both chimpanzee and macaque. A representative sampling of distributions from all DHS is shown in (c), as well as Common DHS sites (d) found in all three species that are matched for signal intensity compared to human DHS gains and human DHS losses. (e) Distribution of species-specific DHS Gains and DHS Losses relative to promoters, introns, 3′ UTR, and intergenic regions. (f) Representative screen shots of human-specific DHS Gains and Losses compared to a Common region.

Figure 2