Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions

Abstract

Stretched histone regions, such as super-enhancers and broad H3K4me3 domains, are associated with maintenance of cell identity and cancer. We connected super-enhancers and broad H3K4me3 domains in the K562 chronic myelogenous leukemia cell line as well as the MCF-7 breast cancer cell line with chromatin interactions. Super-enhancers and broad H3K4me3 domains showed higher association with chromatin interactions than their typical counterparts. Interestingly, we identified a subset of super-enhancers that overlap with broad H3K4me3 domains and show high association with cancer-associated genes including tumor suppressor genes. Besides cell lines, we could observe chromatin interactions by a Chromosome Conformation Capture (3C)-based method, in primary human samples. Several chromatin interactions involving super-enhancers and broad H3K4me3 domains are constitutive and can be found in both cancer and normal samples. Taken together, these results reveal a new layer of complexity in gene regulation by super-enhancers and broad H3K4me3 domains.

FitHiChIP: Identification of significant chromatin contacts from HiChIP data

“…Similar CRISPRi data from the same work identifies no distal (>20kb) enhancer regions for GATA1. For another important gene, TP53, super-enhancer and broad domain analysis coupled with RNA Pol II ChIA-PET data in K562 cells identify two hit regions: one ∼100kb downstream and one ∼150kb upstream of the TP53 promoter [10]. Using EpiSwitch baits, both regions are shown to interact with the TP53 promoter, in addition to K562, in all CML patients (9/9) and nearly all normal subjects.…”

“…To assess whether FitHiChIP connects distal enhancers to their experimentally validated target promoters from H3K27ac HiChIP data, we have compiled a list of loci for which functional data (e.g., CRISPRi) is available together with HiChIP data for the same cell line [8,9,10]. One gene with arguably the most comprehensive data is MYC, for which more than a megabase of surrounding region is tiled with sgRNAs for CRISPRi screen of cellular proliferation in K562 cells.…”

“…This lead to identification of seven distal regions (e1-e7) ranging from 160kb to ∼2Mb in distance to MYC [8]. All of these regions are identified as interacting with MYC promoter through RNA Pol II ChIA-PET [10] and Hi-C, hence are likely to inhibit proliferation through regulating MYC expression. For the ∼400kb region with e1-e4, FitHiChIP identifies all four enhancer regions as interacting with MYC promoter from H3K27ac HiChIP data from K562 cells, whereas HiCCUPS (applied to H3K27ac HiCHIP) [11] only reports the interaction with e2 and hichipper non-specifically reports hundreds of interactions in this locus ( Fig.…”

“…1, 2). Interestingly, both H3K27ac and RNA Pol II ChIA-PET [12,10] also miss these two interactions.…”

“…. For each competing method or setting, we ask what fraction of reference loops reported by ChIA-PET (H3K27ac [12] and Pol2 [10] for K562 cells, RAD21 for GM12878 [12] and mouse embryonic stem cells [13]) or promoter capture Hi-C (naive CD4 cells [14]) are captured at differing number of loop calls from HiChIP data. In all cases FitHiChIP outperforms hichipper in both sensitivity and specificity ( Fig.…”