The dynamic chromatin architecture of the regenerating liver

Abstract

Background & AimsThe adult liver is the main detoxification organ and is routinely exposed to environmental insults but retains the ability to restore its mass and function upon tissue damage. However, massive injury can lead to liver failure, and chronic injury causes fibrosis, cirrhosis, and hepatocellular carcinoma. Currently, the transcriptional regulation of organ repair in the adult liver is incompletely understood.\n\nMethodsWe isolated nuclei from quiescent as well as repopulating hepatocytes in a mouse model of hereditary tyrosinemia, which recapitulates the injury and repopulation seen in toxic liver injury in humans. We then performed the assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) specifically in repopulating hepatocytes to identify differentially accessible chromatin regions and nucleosome positioning. Additionally, we employed motif analysis to predict differential transcription factor occupancy and validated the in silico results with chromatin immunoprecipitation followed by sequencing (ChIP-seq) for hepatocyte nuclear factor 4 (HNF4) and CCCTC-binding factor (CTCF).\n\nResultsChromatin accessibility in repopulating hepatocytes was increased in the regulatory regions of genes promoting proliferation and decreased in the regulatory regions of genes involved in metabolism. The epigenetic changes at promoters and liver enhancers correspond with regulation of gene expression, with enhancers of many liver function genes displaying a less accessible state during the regenerative process. Moreover, increased CTCF occupancy at promoters and decreased HNF4 binding at enhancers implicate these factors as key drivers of the transcriptomic changes in replicating hepatocytes that enable liver repopulation.\n\nConclusionsOur analysis of hepatocyte-specific epigenomic changes during liver repopulation identified CTCF and HNF4 as key regulators of hepatocyte proliferation and regulation of metabolic programs. Thus, liver repopulation in the setting of toxic injury makes use of both general transcription factors (CTCF) for promoter activation, and reduced binding by a hepatocyte-enriched factor (HNF4) to temporarily limit enhancer activity.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC=\"FIGDIR/small/664862v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (13K):\norg.highwire.dtl.DTLVardef@cefbc3org.highwire.dtl.DTLVardef@f2edc8org.highwire.dtl.DTLVardef@d90be9org.highwire.dtl.DTLVardef@19cf7a9_HPS_FORMAT_FIGEXP M_FIG C_FIG