ABSTRACT
Retinoblastoma protein (pRB) mediates cell-cycle withdrawal and differentiation by interacting with a variety of proteins. RB-Binding Protein 2 (RBP2) has been shown to be a key effector. We sought to determine transcriptional regulation by RBP2 genome-wide by using location analysis and gene expression profiling experiments. We describe that RBP2 shows high correlation with the presence of H3K4me3 and its target genes are separated into two functionally distinct classes: differentiation-independent and differentiation-dependent genes. The former class is enriched by genes that encode mitochondrial proteins, while the latter is represented by cell-cycle genes. We demonstrate the role of RBP2 in mitochondrial biogenesis, which involves regulation of H3K4me3-modified nucleosomes. Analysis of expression changes upon RBP2 depletion depicted genes with a signature of differentiation control, analogous to the changes seen upon reintroduction of pRB. We conclude that, during differentiation, RBP2 exerts inhibitory effects on multiple genes through direct interaction with their promoters.
Subject(s)
Cell Differentiation/genetics , Genome, Human/genetics , Histones/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Lysine/metabolism , Oxidoreductases, N-Demethylating/metabolism , Transcription, Genetic , Tumor Suppressor Proteins/metabolism , Binding Sites , Gene Expression Profiling , Gene Expression Regulation , Genomics , Humans , Methylation , Mitochondria/enzymology , Models, Biological , Nucleosomes/enzymology , Promoter Regions, Genetic/genetics , Protein Binding , Repressor Proteins/metabolism , Retinoblastoma-Binding Protein 2 , Sequence Analysis, DNA , Transcription Factors/metabolismABSTRACT
The transcriptional regulatory networks that specify and maintain human tissue diversity are largely uncharted. To gain insight into this circuitry, we used chromatin immunoprecipitation combined with promoter microarrays to identify systematically the genes occupied by the transcriptional regulators HNF1alpha, HNF4alpha, and HNF6, together with RNA polymerase II, in human liver and pancreatic islets. We identified tissue-specific regulatory circuits formed by HNF1alpha, HNF4alpha, and HNF6 with other transcription factors, revealing how these factors function as master regulators of hepatocyte and islet transcription. Our results suggest how misregulation of HNF4alpha can contribute to type 2 diabetes.
