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Fig. 5 | Genome Biology

Fig. 5

From: HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution

Fig. 5

Analysis of RF resolution TAD and subTAD boundaries in GM12878. Analyses were performed on both Hi-C data resulting from a HindIII (3.4 kb per RF on average (ad)) and a MboI restriction digest (434 bp per RF on average (eh), from Rao et al. [23]). TAD and subTAD boundary predictions were made on IF matrices produced either by HIFI-MRF or a fixed-binning approach (16 RF per bin, i.e., approx. 50 kb per bin for HindIII and 7 kb per bin for MboI). a IF matrices produced by HIFI-MRF (top) and fixed binning (bottom) for a 4-Mb locus surrounding the NEK6 locus (chr9:124999244-128993971). b, f CTCF occupancy as a function of distance to the nearest TAD (b) or subTAD (f) boundary, separately for sites on the forward and reverse strands. Convergent CTCF sites are enriched at both TAD and subTAD boundaries. Shaded band indicate 95% confidence intervals of the estimate of the mean occupancy. c, g Coverage of active promoters (red) and strong enhancers (green) identified by ChromHMM, as a function of the distance to the nearest TAD (c) or subTAD (g) boundary. These regions are very strongly enriched just outside of subTAD boundaries, but less so around TAD boundaries. d, h Occupancy of two transcription factors, FOXM1 and NFIC, as a function of distance to the nearest TAD (b) or subTAD (f) boundary. While most TFs have an occupancy peak at TAD and subTAD boundaries, the extent of the enrichment within TADs varies from low (e.g., FOXM1) to high (e.g., NFIC). e IF matrices produced by HIFI-MRF (top) and fixed binning (bottom) for the 200-kb NEK6 locus (chr9:126879748-127079891). Regulatory regions identified in Huang et al. [62] are marked SE (super enhancer), CE1 (conventional enhancer), and NEK6-TSS1 and NEK6-TSS2 (alternative promoters). Notice how all these regions lie between visible subTADs

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