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E-GEOD-18973 - Global expression analysis of HNF4alpha and HNFgamma-mediated transcriptional control

Status
Released on 22 December 2010, last updated on 27 March 2012
Organism
Homo sapiens
Samples (9)
Array (1)
Protocols (6)
Description
Hepatocyte nuclear factor-4α (HNF4α, NR2A1) is a nuclear receptor which 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 isoforms, 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 semi-quantitative 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 genome-wide 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 is important for an accurate understanding of transcriptional regulation. siRNA-mediated HNF4alpha and HNF4gamma double knockdown in HepG2 cells were analysed by using the Affymetrix GeneChip system in tripricate.
Experiment type
transcription profiling by array 
Contacts
Hiroyuki Aburatani, Kenji Daigo, Makoto Naito, Riuko Ohashi, Satoshi Katayose, Sigeo Ihara, Takao Hamakubo, Takeshi Kawamura, Tatsuhiko Kodama, Toshiya Tanaka, Yoshihiro Ohta
Citation
Proteomic analysis of native hepatocyte nuclear factor-4{alpha} (HNF4{alpha}) isoforms, phosphorylation status, and interactive cofactors. Daigo K, Kawamura T, Ohta Y, Ohashi R, Katayose S, Tanaka T, Aburatani H, Naito M, Kodama T, Ihara S, Hamakubo T. , PMID:21047794
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-18973.idf.txt
Sample and data relationshipE-GEOD-18973.sdrf.txt
Raw data (1)E-GEOD-18973.raw.1.zip
Processed data (1)E-GEOD-18973.processed.1.zip
Array designA-AFFY-44.adf.txt
R ExpressionSetE-GEOD-18973.eSet.r
Links