Fig. 4

Validation of open chromatin sites identified by NicE-seq. a A heat map showing the correlation of NicE-seq peaks in a ±3-kb window with occupancy of H3K4me1, H3K4me3, H3K27ac, RNA pol II, and YY1 across ChIP-seq data from ENCODE for HCT116 cells. Input was used to show lack of enrichment. Plotting a heat map using whole genome bisulfite sequencing data for HCT116 cells showed an inverse correlation between OCSs and CpG methylation. b A heat map showing the correlation of ChIP H3K4me3 peaks in a ±3-kb window with NicE-seq and DNase-seq data sets. c A heat map showing the correlation of ChIP H3K27ac peaks in a ±3-kb window with NicE-seq and DNase-seq data sets. d Metagene plot showing the distribution of sequencing tag densities for high (turquoise), medium (orange), low (purple), and no expression (pink) genes (based on the expression level in the RNA-seq data set) in the NicE-seq experiment in a 2-kb window upstream of the transcription start site (TSS) and downstream of the transcription termination site (TTS). e Metagene plot showing the distribution of sequencing tag densities for high (turquoise), medium (orange), low (purple), and no expression (pink) genes (based on the expression level in RNA-seq data set) in the ChIP RNA pol II experiment in a 2-kb window upstream of the TSS and downstream of the TTS. f Metagene plot showing the distribution of sequencing tag densities for high (turquoise), medium (orange), low (purple), and no expression (pink) genes (based on the expression level in the RNA-seq data set) in a 2-kb window upstream of the TSS and downstream of the TTS in the RNA-seq data set