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Alterations of epigenetic signatures in hepatocyte nuclear factor 4α deficient mouse liver determined by improved ChIP‐qPCR and (h)MeDIP‐qPCR assays (1148.4)
Author(s) -
Zhang Qinghao,
Lei Xiaohong,
Lu Hong
Publication year - 2014
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.28.1_supplement.1148.4
Subject(s) - epigenetics , methylated dna immunoprecipitation , h3k4me3 , dna methylation , epigenomics , histone , histone methylation , biology , microbiology and biotechnology , epigenetic regulation of neurogenesis , histone methyltransferase , ezh2 , hepatocyte nuclear factors , chemistry , gene expression , genetics , promoter , gene
Hepatocyte nuclear factor 4α (HNF4α) is a liver‐enriched transcription factor essential for liver development and function. In hepatocytes, HNF4α regulates a large number of genes important for nutrient/xenobiotic metabolism and cell differentiation and proliferation. Currently, little is known about the epigenetic mechanism of gene regulation by HNF4α. In this study, the global and specific alterations at the selected gene loci of representative histone modifications and DNA methylations were investigated in Hnf4a‐deficient female mouse livers using the improved MeDIP‐, hMeDIP‐ and ChIP‐qPCR assay. Hnf4a deficiency significantly increased hepatic total IPed DNA fragments for histone H3 lysine‐4 dimethylation (H3K4me2), H3K4me3, H3K9me2, H3K27me3 and H3K4 acetylation, but not for H3K9me3, 5‐methylcytosine,or 5‐hydroxymethylcytosine. At specific gene loci, the relative enrichments of histone and DNA modifications were changed to different degree in Hnf4a‐deficient mouse liver. Among the epigenetic signatures investigated, changes in H3K4me3 correlated the best with mRNA expression. Additionally, Hnf4a‐deficient livers had increased mRNA expression of histone H1.2 and H3.3 as well as epigenetic modifiers Dnmt1, Tet3, Setd7, Mllt3, Ehmt2, and Ezh2. In conclusion, the present study provides convenient improved (h)MeDIP‐ and ChIP‐qPCR assays for epigenetic study. Hnf4a deficiency in young‐adult mouse liver markedly alters histone methylation and acetylation, with fewer effects on DNA methylation and 5‐hydroxymethylation. The underlying mechanism may be the induction of epigenetic enzymes responsible for the addition/removal of the epigenetic signatures, and/or the loss of HNF4α per se as a key coordinator for epigenetic modifiers. Grant Funding Source : Supported by NIH grants ES019487, CA143656, and CA159350