Three-dimensional interactions between enhancers and promoters during intestinal differentiation depend upon HNF4

• DOI: 10.1016/j.celrep.2020.108679
• Publication Date: 2021-01-26T15:34:27Z
• Authors: Lei Chen; Weihuan Cao; Rohit Aita; Dennis Aldea; Juan Flores; Nan Gao; Edward M. Bonder; Christopher E. El...; Michael P. Verzi
• Keywords: ChIA-PET; Chromosome conformation capture; Chromatin immunoprecipitation; Enhancer RNAs; ChIP-sequencing

Cells in renewing tissues exhibit dramatic transcriptional changes as they differentiate. The contribution of chromatin looping to tissue renewal is incompletely understood. Enhancer-promoter interactions could be relatively stable cells transition from progenitor differentiated states; alternatively, dynamic the gene expression their loci. intestinal epithelium most rapidly mammalian tissue. Proliferative crypts Lieberkühn sustain a stream that are continually shed into lumen. We apply chromosome conformation capture combined with immunoprecipitation (HiChIP) and sequencing measure enhancer-promoter epithelium. Despite regulation across differentiation axis, we find stable. Functionally, HNF4 transcription factors required for at target genes. Depletion disrupts local looping, histone modifications, expression. This study provides insights regulatory mechanisms governing homeostasis tissues.