Figure 1.

Description of the regulatory annotation calling procedures. (A) Super/typical enhancers are called by using the H3K27ac mark ChIP-seq to assign enhancer elements, stitching elements within 12.5 kb and ranking the stitched segments based on H3K27ac levels. (B) Stretch enhancer calling procedure involves analyzing patterns of multiple histone marks and assigning chromatin state segmentations using ChromHMM, followed by identifying contiguous enhancer chromatin state segments longer than 3 kb. (C) HOT regions are defined as regions with higher TF-binding occupancies than expected. (D) Broad domains are defined as the top 5% of the H3K4me3 ChIP-seq peaks by length. ChIP-seq, chromatin immunoprecipitation-sequencing; HMM, hidden Markov model; HOT, high-occupancy target; ROSE, rank ordering of super enhancers; TF, transcription factor.