Fig. 7
From: Links between DNA methylation and nucleosome occupancy in the human genome
Characterization of chromatin at unmethylated and methylated conserved transcription factor binding sites. All conserved transcription factor binding sites (TFBSs) from the UCSC genome browser were divided into unmethylated and methylated sites (see “Methods” section). a Using NOMe-seq, BS-seq, and ENCODE ChIP-seq data from HCT116 cells, nucleosome occupancy, DNA methylation levels, and DNase-seq and H3K27ac signals were aligned to unmethylated and methylated conserved TFBSs. b Average uGCH/GCH fractions were also computed from forward and reverse complement sequences aligned to these unmethylated and methylated conserved TFBSs. c Similar to a, nucleosome occupancy, DNA methylation levels, and DNase-seq, H3K27ac, and SP1 signals were aligned to unmethylated and methylated SP1 conserved TFBSs. d Using ENCODE ChIP-seq data for 10 transcription factors, including SP1, average signals were plotted with respect to their corresponding unmethylated and methylated conserved TFBSs. In the heatmaps, average signals were computed in 51 21-bp bins surrounding each conserved site. Scales for DNase-seq, H3K27ac, and the transcription factors represent occupancy levels in reads per million