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PMID: 24427299 Published · epublish English Journal Article Research Support, N.I.H., Extramural

Alterations of epigenetic signatures in hepatocyte nuclear factor 4α deficient mouse liver determined by improved ChIP-qPCR and (h)MeDIP-qPCR assays.

PloS one ·Vol. 9 ·No. 1 ·2014-00-00 ·Pages e84925

Zhang Q, Lei X, Lu H

Abstract

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, Kmt2c, 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.

MeSH Terms
Animals Chromatin Immunoprecipitation DNA Methylation Epigenesis, Genetic Epigenomics/methods Female Hepatocyte Nuclear Factor 4/deficiency,genetics Histones/metabolism Liver/metabolism Mice Mice, Knockout RNA, Messenger/genetics Real-Time Polymerase Chain Reaction Reproducibility of Results Sensitivity and Specificity
Chemicals
Hepatocyte Nuclear Factor 4 Histones Hnf4a protein, mouse RNA, Messenger
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Zhang Qinghao
Department of Pharmacology, SUNY Upstate Medical University, Syracuse, New York, United States of America.
Lei Xiaohong
Department of Pharmacology, SUNY Upstate Medical University, Syracuse, New York, United States of America.
Lu Hong
Department of Pharmacology, SUNY Upstate Medical University, Syracuse, New York, United States of America.
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Article Info
Journal
PloS one
Abbr.
PLoS One
ISSN
1932-6203
DOI
10.1371/journal.pone.0084925
Published
2014-00-00
Epub
2014-00-10
Pages
e84925
Language
English
Region
United States
NLM ID
101285081
PMCID
PMC3888413
Subset
IM
Grants
NCI NIH HHS · R03 CA159350 · United States
NIEHS NIH HHS · R01 ES019487 · United States
NCI NIH HHS · CA143656 · United States
NCI NIH HHS · CA159350 · United States
NIEHS NIH HHS · ES019487 · United States
NCI NIH HHS · R03 CA143656 · United States
External Links
PubMed source DOI: 10.1371/journal.pone.0084925 PMC Full Text View journal details
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