Epigenetic marks and chromatin environment at IS. (A,B) Specific chromatin marks/factors associated with open chromatin-2 (blue boxes) and Polycomb complexes (brown boxes) at initiation sites. (A) Distribution of chromatin marks/factors relative to IS (dark green) and IZ (light green). (B) ChIP-seq signals for H3K4me3, H3K9ac, H3K27me3, and SUZ12 around ±7 kb from IS. (C) Hierarchical clustering of Pearson correlations between pairs of marks and/or chromatin factors for all IS. Marks and factors in the heatmap are organized according to the clustering described in Methods. Positive correlations are symbolized by a gradation of red that results from the localization of pairs of marks/factors at individual IS. Negative correlations are symbolized by a gradation of blue. Four significant groups of chromatin mark/factor are highlighted on the right: Open 1 chromatin marks/factors group (mostly associated with transcription initiation); Open 2 chromatin marks group (globally linked to decondensed chromatin); Enhancer marks (Enh.); and Polycomb group mark/factors (PcG). (D) More than 80% of H3K27me3 marks at IZ are associated with PRC1 or PRC2 proteins or are inside bivalent domains. (E) Overlap between marks/factors and origins.
