Proteomic analysis of native hepatocyte nuclear factor-4α (HNF4α) isoforms, phosphorylation status, and interactive cofactors

Kenji Daigo, Takeshi Kawamura, Yoshihiro Ohta, Riuko Ohashi, Satoshi Katayose, Toshiya Tanaka, Hiroyuki Aburatani, Makoto Naito, Tatsuhiko Kodama, Sigeo Ihara, Takao Hamakubo

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

Hepatocyte nuclear factor-4α (HNF4α, NR2A1) is a nuclear receptor that has a critical role in hepatocyte differentiation and the maintenance of homeostasis in the adult liver. However, a detailed understanding of native HNF4α in the steady-state remains to be elucidated. Here we report the native HNF4α isoform, phosphorylation status, and complexes in the steady-state, as shown by shotgun proteomics in HepG2 hepatocarcinoma cells. Shotgun proteomic analysis revealed the complexity of native HNF4α, including multiple phosphorylation sites and inter-isoform heterodimerization. The associating complexes identified by label-free semiquantitative proteomic analysis include the following: the DNA-dependent protein kinase catalytic subunit, histone acetyltransferase complexes, mRNA splicing complex, other nuclear receptor coactivator complexes, the chromatin remodeling complex, and the nucleosome remodeling and histone deacetylation complex. Among the associating proteins, GRB10 interacting GYF protein 2 (GIGYF2, PERQ2) is a new candidate cofactor in metabolic regulation. Moreover, an unexpected heterodimerization of HNF4α and hepatocyte nuclear factor-4γ was found. A biochemical and genomewide analysis of transcriptional regulation showed that this heterodimerization activates gene transcription. The genes thus transcribed include the cell death-inducing DEF45-like effector b (CIDEB) gene, which is an important regulator of lipid metabolism in the liver. This suggests that the analysis of the distinctive stoichiometric balance of native HNF4α and its cofactor complexes described here are important for an accurate understanding of transcriptional regulation.

Original languageEnglish
Pages (from-to)674-686
Number of pages13
JournalJournal of Biological Chemistry
Volume286
Issue number1
DOIs
Publication statusPublished - Jan 7 2011

Fingerprint

Hepatocyte Nuclear Factor 4
Phosphorylation
Proteomics
Protein Isoforms
Genes
Firearms
GRB10 Adaptor Protein
Liver
Nuclear Receptor Coactivators
DNA-Activated Protein Kinase
Histone Acetyltransferases
Chromatin Assembly and Disassembly
Nucleosomes
Hep G2 Cells
Cell death
Transcription
Cytoplasmic and Nuclear Receptors
Systems Analysis
Lipid Metabolism
Histones

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Proteomic analysis of native hepatocyte nuclear factor-4α (HNF4α) isoforms, phosphorylation status, and interactive cofactors. / Daigo, Kenji; Kawamura, Takeshi; Ohta, Yoshihiro; Ohashi, Riuko; Katayose, Satoshi; Tanaka, Toshiya; Aburatani, Hiroyuki; Naito, Makoto; Kodama, Tatsuhiko; Ihara, Sigeo; Hamakubo, Takao.

In: Journal of Biological Chemistry, Vol. 286, No. 1, 07.01.2011, p. 674-686.

Research output: Contribution to journalArticle

Daigo, K, Kawamura, T, Ohta, Y, Ohashi, R, Katayose, S, Tanaka, T, Aburatani, H, Naito, M, Kodama, T, Ihara, S & Hamakubo, T 2011, 'Proteomic analysis of native hepatocyte nuclear factor-4α (HNF4α) isoforms, phosphorylation status, and interactive cofactors', Journal of Biological Chemistry, vol. 286, no. 1, pp. 674-686. https://doi.org/10.1074/jbc.M110.154732
Daigo, Kenji ; Kawamura, Takeshi ; Ohta, Yoshihiro ; Ohashi, Riuko ; Katayose, Satoshi ; Tanaka, Toshiya ; Aburatani, Hiroyuki ; Naito, Makoto ; Kodama, Tatsuhiko ; Ihara, Sigeo ; Hamakubo, Takao. / Proteomic analysis of native hepatocyte nuclear factor-4α (HNF4α) isoforms, phosphorylation status, and interactive cofactors. In: Journal of Biological Chemistry. 2011 ; Vol. 286, No. 1. pp. 674-686.
@article{6a6f8e95059b4262aa3da8970c828add,
title = "Proteomic analysis of native hepatocyte nuclear factor-4α (HNF4α) isoforms, phosphorylation status, and interactive cofactors",
abstract = "Hepatocyte nuclear factor-4α (HNF4α, NR2A1) is a nuclear receptor that has a critical role in hepatocyte differentiation and the maintenance of homeostasis in the adult liver. However, a detailed understanding of native HNF4α in the steady-state remains to be elucidated. Here we report the native HNF4α isoform, phosphorylation status, and complexes in the steady-state, as shown by shotgun proteomics in HepG2 hepatocarcinoma cells. Shotgun proteomic analysis revealed the complexity of native HNF4α, including multiple phosphorylation sites and inter-isoform heterodimerization. The associating complexes identified by label-free semiquantitative proteomic analysis include the following: the DNA-dependent protein kinase catalytic subunit, histone acetyltransferase complexes, mRNA splicing complex, other nuclear receptor coactivator complexes, the chromatin remodeling complex, and the nucleosome remodeling and histone deacetylation complex. Among the associating proteins, GRB10 interacting GYF protein 2 (GIGYF2, PERQ2) is a new candidate cofactor in metabolic regulation. Moreover, an unexpected heterodimerization of HNF4α and hepatocyte nuclear factor-4γ was found. A biochemical and genomewide analysis of transcriptional regulation showed that this heterodimerization activates gene transcription. The genes thus transcribed include the cell death-inducing DEF45-like effector b (CIDEB) gene, which is an important regulator of lipid metabolism in the liver. This suggests that the analysis of the distinctive stoichiometric balance of native HNF4α and its cofactor complexes described here are important for an accurate understanding of transcriptional regulation.",
author = "Kenji Daigo and Takeshi Kawamura and Yoshihiro Ohta and Riuko Ohashi and Satoshi Katayose and Toshiya Tanaka and Hiroyuki Aburatani and Makoto Naito and Tatsuhiko Kodama and Sigeo Ihara and Takao Hamakubo",
year = "2011",
month = "1",
day = "7",
doi = "10.1074/jbc.M110.154732",
language = "English",
volume = "286",
pages = "674--686",
journal = "Journal of Biological Chemistry",
issn = "0021-9258",
publisher = "American Society for Biochemistry and Molecular Biology Inc.",
number = "1",

}

TY - JOUR

T1 - Proteomic analysis of native hepatocyte nuclear factor-4α (HNF4α) isoforms, phosphorylation status, and interactive cofactors

AU - Daigo, Kenji

AU - Kawamura, Takeshi

AU - Ohta, Yoshihiro

AU - Ohashi, Riuko

AU - Katayose, Satoshi

AU - Tanaka, Toshiya

AU - Aburatani, Hiroyuki

AU - Naito, Makoto

AU - Kodama, Tatsuhiko

AU - Ihara, Sigeo

AU - Hamakubo, Takao

PY - 2011/1/7

Y1 - 2011/1/7

N2 - Hepatocyte nuclear factor-4α (HNF4α, NR2A1) is a nuclear receptor that has a critical role in hepatocyte differentiation and the maintenance of homeostasis in the adult liver. However, a detailed understanding of native HNF4α in the steady-state remains to be elucidated. Here we report the native HNF4α isoform, phosphorylation status, and complexes in the steady-state, as shown by shotgun proteomics in HepG2 hepatocarcinoma cells. Shotgun proteomic analysis revealed the complexity of native HNF4α, including multiple phosphorylation sites and inter-isoform heterodimerization. The associating complexes identified by label-free semiquantitative proteomic analysis include the following: the DNA-dependent protein kinase catalytic subunit, histone acetyltransferase complexes, mRNA splicing complex, other nuclear receptor coactivator complexes, the chromatin remodeling complex, and the nucleosome remodeling and histone deacetylation complex. Among the associating proteins, GRB10 interacting GYF protein 2 (GIGYF2, PERQ2) is a new candidate cofactor in metabolic regulation. Moreover, an unexpected heterodimerization of HNF4α and hepatocyte nuclear factor-4γ was found. A biochemical and genomewide analysis of transcriptional regulation showed that this heterodimerization activates gene transcription. The genes thus transcribed include the cell death-inducing DEF45-like effector b (CIDEB) gene, which is an important regulator of lipid metabolism in the liver. This suggests that the analysis of the distinctive stoichiometric balance of native HNF4α and its cofactor complexes described here are important for an accurate understanding of transcriptional regulation.

AB - Hepatocyte nuclear factor-4α (HNF4α, NR2A1) is a nuclear receptor that has a critical role in hepatocyte differentiation and the maintenance of homeostasis in the adult liver. However, a detailed understanding of native HNF4α in the steady-state remains to be elucidated. Here we report the native HNF4α isoform, phosphorylation status, and complexes in the steady-state, as shown by shotgun proteomics in HepG2 hepatocarcinoma cells. Shotgun proteomic analysis revealed the complexity of native HNF4α, including multiple phosphorylation sites and inter-isoform heterodimerization. The associating complexes identified by label-free semiquantitative proteomic analysis include the following: the DNA-dependent protein kinase catalytic subunit, histone acetyltransferase complexes, mRNA splicing complex, other nuclear receptor coactivator complexes, the chromatin remodeling complex, and the nucleosome remodeling and histone deacetylation complex. Among the associating proteins, GRB10 interacting GYF protein 2 (GIGYF2, PERQ2) is a new candidate cofactor in metabolic regulation. Moreover, an unexpected heterodimerization of HNF4α and hepatocyte nuclear factor-4γ was found. A biochemical and genomewide analysis of transcriptional regulation showed that this heterodimerization activates gene transcription. The genes thus transcribed include the cell death-inducing DEF45-like effector b (CIDEB) gene, which is an important regulator of lipid metabolism in the liver. This suggests that the analysis of the distinctive stoichiometric balance of native HNF4α and its cofactor complexes described here are important for an accurate understanding of transcriptional regulation.

UR - http://www.scopus.com/inward/record.url?scp=78650950537&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78650950537&partnerID=8YFLogxK

U2 - 10.1074/jbc.M110.154732

DO - 10.1074/jbc.M110.154732

M3 - Article

C2 - 21047794

AN - SCOPUS:78650950537

VL - 286

SP - 674

EP - 686

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

SN - 0021-9258

IS - 1

ER -