Supplementary Figure 5: Developmental and lineage specificity of induced gene-linked enhancers.
(a) Heat map of H3K27ac ChIP–seq signal at enhancers contacting induced genes and exhibiting gained H3K27ac in differentiation. z score is calculated for ChIP–seq signal across rows (cell types). Column labels correspond to the following: ES, H1 hESC human embryonic stem cells; GM, GM12878 immortalized B lymphocytes; HS, human skeletal muscle cells and myoblasts; HU, HUVEC human umbilical vein endothelial cells; LF, NHLF normal human lung fibroblasts; OS, OSTEO human primary osteoblasts; HM, HMEC human mammary epithelial cells; NH, NHEK normal human epidermal keratinocytes; D0, day 0; D3, day 3; D6, day 6. (b) Box-and-whisker plots representing the heat map in d (two-sided KS test, D0 versus hES P = 7.292 × 10−9, D3 versus hES P < 2.2 × 10−16, D6 versus hES P < 2.2 × 10−16). (c) Similar to d, including enhancers contacting induced genes and exhibiting no significant dynamics of H3K27ac in differentiation. (d) Box-and-whisker plots representing the heat map in f (two-sided KS test, D0 versus hES P < 2.2 × 10−16, D3 versus hES P < 2.2 × 10−16, D6 versus hES P < 2.2 × 10−16). (e) Normalized CHi-C read count profile for contacts from the DSC2 promoter (normalized to total reads associated with the viewpoint fragment in each condition). The gray dotted line marks the position of the viewpoint fragment. NHEK and hESC H3K27ac signal tracks and peak calls are taken directly from the ENCODE portal of the UCSC Genome Browser. (f) Box-and-whisker plots representing CHi-C read count z scores for induced gene-associated contacts gained in epidermal differentiation (two-sided KS test, D6 versus hES P < 2.2 × 10−16, D3 versus hES P < 2.2 × 10−16). (g) Similar to f for induced gene-associated contacts that are stable in epidermal differentiation (two-sided KS test, D0 versus hES P < 2.2 × 10−16, D3 versus hES P < 2.2 × 10−16, D6 versus hES P < 2.2 × 10−16). (h) Similar to e, for profiles of the SOX21 promoter, which is expressed specifically in hESCs. KS test, **P < 1 × 10−5, ***P < 1 × 10−15.
