Supplementary Figure 4: Enrichment of the FOXA1 DNA repair complex at distinct epigenetic states.
From: Nucleation of DNA repair factors by FOXA1 links DNA demethylation to transcriptional pioneering
Enrichment of the FOXA1 complex at distinct epigenetic states. (a) Chromatin state annotation was produced from ChromHMM using ChIP-seq data on H3K4me1, H3K4me3, H3K9me3, H3K27me3, H3K36me3, and H3K27ac in MCF-7 cells. This model distinguished seven broad classes of chromatin state, referred to as follows: state E1, Polycomb-repressed state enriched for characteristic H3K27me3; state E2, heterochromatin state without enrichment for any of these marks; state E3, repressive state enriched for H3K9me3; state E4, transcribed state enriched with H3K36me3 at gene bodies; state E5, enhancer state strongly enriched for the enhancer markers H3K27ac and H3K4me1; state E6, enhancer state weakly enriched for H3K27ac; state E7, promoter state strongly enriched for H3K4me3 and moderately enriched for H3K27ac. Emission and transition parameters for the multivariate hidden Markov model are displayed as a heat map. (b) The heat map indicates the relative percentage of the genome represented by each chromatin state and the relative fold enrichment of the full set of FOXA1 complex binding sites for the states determined in a. (c) The entire set of FOXA1 complex binding sites were grouped on the basis of their intersection with the epigenomic states determined in a. Average profiles of FOXA1 and POLB in these seven subgroups were plotted.
