The dynamic chromatin architecture of the regenerating liver
| Autor: | Klaus H. Kaestner, Kirk J. Wangensteen, Yue J. Wang, Adam M. Zahm, Amber W. Wang, Ashleigh Morgan |
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| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
CCCTC-Binding Factor CTCF CCCTC-binding factor Hydrolases ATAC-seq Epigenesis Genetic Mice ChIP-Seq 0302 clinical medicine Hepatocyte RNA-Seq Promoter Regions Genetic GFP green fluorescence protein Original Research Epigenomics Mice Knockout Chromatin Accessibility 0303 health sciences YY1 Yin Yang 1 Tyrosinemias FAH fumarylacetoacetate hydrolase Gastroenterology High-Throughput Nucleotide Sequencing Chromatin Liver regeneration Cell biology Hepatocyte nuclear factors Enhancer Elements Genetic medicine.anatomical_structure Hepatocyte Nuclear Factor 4 Liver PHx partial hepatectomy INTACT isolation of nuclei tagged in specific cell types NF-Y nuclear transcription factor Y qPCR quantitative polymerase chain reaction 030211 gastroenterology & hepatology SDS sodium dodecyl sulfate PBS phosphate-buffered saline TRAP translating ribosome affinity purification ZBTB3 zinc finger and BTB domain-containing protein 3 ATAC-Seq Biology HNF4α hepatocyte nuclear factor 4α 03 medical and health sciences TRAP-Seq NTBC 2-(2-nitro-4-trifluoromethylbenzoyl)-1 3-cyclohexanedione medicine Animals Humans ATAC-seq assay for transposase accessible chromatin with high-throughput sequencing Enhancer HNF4α Cell Proliferation 030304 developmental biology Cell Nucleus TRAP-seq translating ribosome affinity purification followed by RNA sequencing Hepatology Gene Expression Profiling ChIP-seq chromatin immunoprecipitation followed by high-throughput sequencing FDR false-discovery rate CTCF Liver Regeneration Disease Models Animal 030104 developmental biology Hepatocytes TSS transcription start site Liver function Chromatin immunoprecipitation 030217 neurology & neurosurgery DAPI 4′ 6-diamidino-2-phenylindole |
| Zdroj: | Cellular and Molecular Gastroenterology and Hepatology |
| DOI: | 10.1101/664862 |
| Popis: | Background & Aims The adult liver is the main detoxification organ and routinely is exposed to environmental insults but retains the ability to restore its mass and function upon tissue damage. However, extensive 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. Methods We 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 human beings. We then performed the assay for transposase accessible chromatin with high-throughput sequencing specifically in repopulating hepatocytes to identify differentially accessible chromatin regions and nucleosome positioning. In addition, we used motif analysis to predict differential transcription factor occupancy and validated the in silico results with chromatin immunoprecipitation followed by sequencing for hepatocyte nuclear factor 4α (HNF4α) and CCCTC-binding factor (CTCF). Results Chromatin 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 the regulation of gene expression, with enhancers of many liver function genes showing a less accessible state during the regenerative process. Moreover, increased CTCF occupancy at promoters and decreased HNF4α binding at enhancers implicate these factors as key drivers of the transcriptomic changes in replicating hepatocytes that enable liver repopulation. Conclusions Our analysis of hepatocyte-specific epigenomic changes during liver repopulation identified CTCF and HNF4α 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 (HNF4α) to temporarily limit enhancer activity. All sequencing data in this study were deposited to the Gene Expression Omnibus database and can be downloaded with accession number GSE109466. Graphical abstract |
| Databáze: | OpenAIRE |
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