Fig. 3

CapSTARR-seq Functional Enhancer Profiling. a CapSTARR-seq experimental workflow. b H3K27ac (red) and CapSTARR-seq (blue) profiles at the ABHD11, CLDN3, and CLDN4 loci in OCUM1 cells. The top blue track depicts CapSTARR-seq signals merged from three CapSTARR-seq replicates. Black boxes denote CapSTARR-seq probes. c Circos visualization of CapSTARR-seq signals across the human genome in SNU16 (the inner circle) and OCUM1 cells (the outer circle). HDAC1, MYC, and CD44 are highlighted as genes associated with CapSTARR-seq high enhancers. d Chromatin state discovery and characterization. The leftmost panel displays a ChomHMM heatmap of emission parameters where each row corresponds to a different state and each column a different histone mark. Shown to its left are candidate state descriptions for each state followed by a state abbreviation. The heatmap in the middle displays the overlap enrichment for various external genomic annotations. The rightmost heatmap shows fold enrichment for each state near TSSs. e Differences in CapSTARR-seq signals (log₂ RPKM) in six enhancer-associated chromatin states called from ChromHMM in OCUM1 (left) and SNU16 (right). f Distribution of H3K27ac active and inactive elements in CapSTARR-seq enriched regions (CaPERs) in OCUM1 and SNU16 cells. g Differences in H3K4me1 ChIP-seq and ATAC-seq peak enrichment at H3K27ac active and inactive CaPERs. Error bars indicate two independent biological replicates. h Distribution of OCUM1/SNU16 H3K27ac inactive CaPERs in the “open” state across 17 cell lines. Red regions denote OCUM1/SNU16 H3K27ac inactive CaPERs located in open chromatin in any of 17 cell lines. Gray regions denote OCUM1/SNU16 H3K27ac inactive CaPERs located in closed chromatin across all the cell lines. i Differences in CapSTARR-seq signals (log₂ RPKM) in enhancer categories in OCUM1 cells. P values: Mann–Whitney U test. j Differences in TF binding sites over enhancer categories. The number of TF binding sites over an enhancer was calculated using the ReMap database. P values: Mann–Whitney U test