Fig. 1

Genome-wide promoter-enhancer mapping with HiCap. a Length distribution of sequence-captured promoter regions in mESCs by HiCap and CHi-C based on either a 4-cutter (turquoise) or a 6-cutter (green). b Length distribution of distal regions identified by HiCap/CHi-C 4-cutter (blue), 6-cutter (purple) and ChIA-PET (orange) in mESCs. c Snapshot of observed promoter-anchored interactions for three genes (Sco2, Arsa and Shank3) in HiCap and CHi-C data, overlaid with genome-wide enhancer and chromatin marks. d Detailed zoom-in on one distal region identified by HiCap/CHi-C (6-cutter), which contains multiple smaller distal regions identified by HiCap/CHi-C (4-cutter). Promoters and distal regions are color coded as in (a, b). Gene names indicate which gene the distal region is interacting with. In both cases, these distal regions are interacting with same genes (Sco2, Arsa and Shank3). e Signal (observed overlap divided by expected) between HiCap promoter-anchored interactions mapping to distal regions and published genome-wide enhancers (blue), chromatin marks for silent genes (turquoise) and promoter marks (gray) in mESCs. HiCap distal regions were classified into expressed [>3 RPKM (reads per kilobase of gene model and million uniquely mapped reads)] and silent (≤0.3 RPKM) by the expression of their target genes. Significant (χ ² test) comparisons are indicated with asterisks: *P < 0.05, **P < 0.001; ***P < 10⁻¹⁰; ns not significant. f Fraction of observed HiCap interactions contained within topologically associating domains (TADs), as a function of the interaction distance and compared with expected