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. Author manuscript; available in PMC: 2019 Mar 28.
Published in final edited form as: Cell Syst. 2018 Feb 14;6(3):381–394.e7. doi: 10.1016/j.cels.2018.01.002

Figure 2. Rapid turnover of enhancer elements.

Figure 2

A) Integrative Genome Viewer diagram of the PRDM1 regulatory region in both mouse (top) and human (bottom) displaying the data used in this study. Tracks display from top to bottom: sequence conservation as estimated by SiPhy (Omega), RefSeq gene annotations, RNA-Seq coverage for unstimulated and one hour post-LPS, overlaid H3K4Me3, ATAC and H3K27ac coverage. Human data in reverse orientation, yellow boxes and curved lines indicate conserved H3K27ac peaks (regulatory regions with conserved activity: promoters or ECAs). Inlets show individual tracks for H3K27ac time course after LPS stimulation. Red boxes indicate H3K27ac peaks with species-specific activity. B) Proportion of regulatory regions with conserved activity: conserved promoters or ECAs, mouse-specific with clear human homologous sequence (mapped promoters or ESPA) and mouse-specific with no clear homologous sequence in human (unmapped promoters or ESPA) C) Average signal for mouse H3K27ac (left) and ATAC-Seq (right) signal over regulatory elements. Enhancer (top) H3K27ac or ATAC-Seq signal is centered in open regions, defined by ATAC-Seq peaks. Promoter (bottom) H3K27ac or ATAC-Seq signal is centered in the TSS. Data is shown for conserved enhancers and promoters (yellow), mouse-specific enhancers and promoters (red) and all other mouse genome coordinates for mapped human-specific enhancers and promoters (black). RPM = reads per million mapped reads D) Fraction of mouse enhancers that are active (pre-established) in bone marrow (mBM) cells and enhancers that are mDC specific, and fraction of mBM pre-established or mDC specific enhancers that are conserved (ECA).