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HNF4A is essential for the active epigenetic state at enhancers in mouse liver

Posted April 23, 2019 | Publications

Thakur A, Wong JCH, Wang EY, Lotto J, Kim D, Cheng JC, Mingay M, Cullum R, Moudgil V, Ahmed N, Tsai SH, Wei W, Walsh CP, Stephan T, Bilenky M, Fuglerud BM, Karimi MM, Gonzalez FJ, Hirst M, Hoodless PA. Hepatology. 2019 Apr 1. doi: 10.1002/hep.30631. [Epub ahead of print]


Cell fate determination is influenced by interactions between master transcription factors (TFs) and cis-regulatory elements. Hepatocyte nuclear factor 4 alpha (HNF4A), a liver-enriched TF, acts as a master controller in specification of hepatic progenitor cells by regulating a network of TFs to control the onset of hepatocyte cell fate. Using analysis of genome-wide histone modifications, DNA methylation and hydroxymethylation in mouse hepatocytes, we show that HNF4A occupies active enhancers in hepatocytes and is essential for active histone and DNA signatures, especially H3K27ac and 5-hydroxymethylcytosine (5hmC). In mice lacking HNF4A protein in hepatocytes, we observed a decrease in both H3K27ac and hydroxymethylation at regions bound by HNF4A. Mechanistically, HNF4A-associated hydroxymethylation (5hmC) requires its interaction with TET3, a protein responsible for oxidation from 5mC to 5hmC. Furthermore, HNF4A regulates TET3 expression in liver by directly binding to an enhancer region. In conclusion, we identified that HNF4A is required for the active epigenetic state at enhancers that amplifies transcription of genes in hepatocytes. This article is protected by copyright. All rights reserved.