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

Figure 4

Comparison of human DHS site gains and losses to DNase-seq data from other human cell types.

The log of the DNase-seq signal intensity value, defined as the maximum parzen score (output of F-seq) for each of the coordinates that are represented along the x-axis, are represented as a heatmap in these figures. The color red represents a higher score, and thus a relatively higher DNase-seq signal, and the color blue represents a lower score. (a) 836 DHS sites were identified as differentially open (human DHS gain) in human fibroblasts compared to chimpanzee/macaque fibroblasts. These regions from Human Fibroblasts (Hu Fibro 1–3) were compared to DNase-seq data generated from 27 other human cell types (Table S3). Additional human skin fibroblast samples (listed in black) are highly similar, while some non-fibroblast cell types show less but substantial overlap and the remaining cell types show much less overlap. Only a small fraction of DHS sites were active in all 27 cell lines (Figure S5). Sites with evidence for positive selection are indicated in the horizontal bar above the heatmap. The distribution appears roughly uniform. (b) 286 DHS sites identified as differentially closed (human DHS loss) compared to chimp and macaque fibroblasts. (c) DNase-seq signal values for Common regions representing DHS sites in all three species. More than 50% of Common regions are also DHS sites in other human tissues. (d, e, f) DNase-seq values for same regions as (a, b, c), but DNase data is from orthologous region from chimpanzee and macaque fibroblasts.

Figure 4

doi: https://doi.org/10.1371/journal.pgen.1002789.g004