Global analysis of the DHS landscape of mouse CNS. (A) Comparison of DHSs to other epigenetic marks at the Nefl locus. DNase I cleavage patterns are shown for the E14.5 mouse brain (red) and ChIP-seq for H3K4me1 (green), H3K4me3 (blue), H3K27ac (purple), and H3K27me3 (yellow). Solid bars under the ChIP-seq signals represent peak calls. The top row of solid bars under the DNase I signal represents hotspot calls (see Methods), and the bottom row represents DHS peak calls. (B) The percentage of ChIP-seq peaks of different histone modifications that overlap with DHSs in E14.5 brain. DHSs from the E14.5 mouse brain to the H3K27ac ChIP-seq data at the same age shows close to 100% (99.6%) of the H3K27ac sites overlap with those identified by a DHS. (C) Distribution of DHSs present in adult brain and in CNS-core DHSs relative to genomic features. (D, E) Comparison of DNase I hypersensitivity in E14.5 mouse brain to recent P300 or H3K27ac ChIP-seq [15, 28, 29] studies of developing mouse cerebral cortex. (D) Correspondence between DNase I hypersensitivity, H3K27ac ChIP-seq, and two P300 ChIP-seq experiments. Peak calls for these three related studies near the Olig1 and Olig2 genes, along with the DNase I hotspots for E14.5 brain. P300 visel, peak calls for P300 ChIP-seq performed by ; P300 wenger, peak calls for P300 ChIP-seq performed by ; H3K27ac, peak calls for H3K27ac ChIP-seq ; DHS, DNase I hotspots; DNase, DNase I signal track. (E) Genome-wide comparisons for correspondence of the P300 ChIP-seq and DNase I hotspots showing >80% of the P300 peaks overlap with DNase I hotspots. Bar values indicate the percent of overlap between the indicated datasets.