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Transcription profiling of mouse primary embryonic fibroblasts reveals the retinoblastoma binding protein RBP2 is an H3K4 demethylase

ABSTRACT: The roles of histone demethylase RBP2 in gene expression were assessed using gene expression profiling experiments with wild type and RBP2-/- primary MEFs. Several cytokine genes including SDF1 and Kit ligand were upregulated upon inactivation of RBP2. Experiment Overall Design: Total RNA were extracted from two independent lines of wild type and RBP2 primary MEFs at passage 3 and analyzed for gene expression profiles using Affymetrix platform.

ORGANISM(S): Mus musculus

SUBMITTER: Qin Yan

PROVIDER: E-GEOD-6945 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The retinoblastoma binding protein RBP2 is an H3K4 demethylase.

Klose Robert J RJ Yan Qin Q Tothova Zuzana Z Yamane Kenichi K Erdjument-Bromage Hediye H Tempst Paul P Gilliland D Gary DG Zhang Yi Y Kaelin William G WG

Cell 20070222 5

Changes in histone methylation status regulate chromatin structure and DNA-dependent processes such as transcription. Recent studies indicate that, analogous to other histone modifications, histone methylation is reversible. Retinoblastoma binding protein 2 (RBP2), a nuclear protein implicated in the regulation of transcription and differentiation by the retinoblastoma tumor suppressor protein, contains a JmjC domain recently defined as a histone demethylase signature motif. Here we report that ...[more]

PMID: 17320163

Similar Datasets

The Retinoblastoma Binding Protein RBP2 is an H3K4 demethylase

Project description:The roles of histone demethylase RBP2 in gene expression were assessed using gene expression profiling experiments with wild type and RBP2-/- primary MEFs. Several cytokine genes including SDF1 and Kit ligand were upregulated upon inactivation of RBP2. Keywords: mouse embryonic fibroblasts, gene expression profiling, microarray, Affymetrix Mouse Genome 430 2.0, cell type comparison

2007-02-22 | GSE6945 | GEO

Changes in H3K4 methylation in KDM5A/JARID1A/RBP2 knockout cells.

Project description:We sought to determine H3K4me3 distribution in mouse embryonic stem (ES) cells deficient for RBP2 compared with wild-type cells. RBP2 modifies methylated lysine residues on histone tails. As a result of this analysis, we identified genomic regions with changed H3K4me3 status and described these in gene ontology (GO) categories. Examination of histone methylation in the absence of histone demethylase RBP2

2015-08-12 | E-GEOD-28348 | biostudies-arrayexpress

Changes in H3K4 methylation in KDM5A/JARID1A/RBP2 knockout cells.

2015-08-12 | GSE28348 | GEO

Expression data in H1299 after retinoblastoma binding protein-2 (RBP2) knockdown

2013-06-20 | GSE41443 | GEO

Expression data in H1299 after retinoblastoma binding protein-2 (RBP2) knockdown

Project description:To identify genes whose expression was affected by RBP2, we performed gene expression microarray analysis in control and RBP2 depletion human lung cancer cell line. Two individual shRNA (RBP2 KD1 and RBP2 KD2) were used to limit potential off-target effects. One scramble short haripin RNA (shRNA) and two individual shRNAs to the human RBP2 gene (RBP2 KD1 and RBP2 KD2) were used. Two replicates per group were used. H1299 cells were infected with lentivirus which carriy shRNAs for 3 days. RNA was isloated by Trizol reagent and analyzed by bioanalyzer. Microarray experiments was performed by the Affymetrix Gene Expression Service Laboratory at Academia Sinica.

2013-06-20 | E-GEOD-41443 | biostudies-arrayexpress

Histone demethylase RBP2 is critical for breast cancer progression and metastasis

2014-02-27 | GSE49119 | GEO

Histone demethylase RBP2 is critical for breast cancer progression and metastasis

Project description:To determine the roles of RBP2 in breast cancer metastasis, MDA-MD-231 cells were transfected with siRNAs against RBP2 or luciferase control, followed with gene expression microarray analysis and gene set enrichment analysis. These analyses revealed that RBP2 knockdown significantly decreased expression of genes linked to breast cancer metastasis to lung. Total RNA obtained from the breast cancer cell line MDA-MB231 72 hours after transfection with siRNA targeting KDM5A/RBP2/JARID1A, and targeting Luceferase gene as a control.

2014-02-27 | E-GEOD-49119 | biostudies-arrayexpress

Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

Project description: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.

| S-EPMC3003864 | biostudies-literature

SAOS-2 cells, RBP2 knockdown or pRB overexpression

Project description:RBP2 is downstream of pRB pathway We used gene expression profiling experiments to investigate if gene expression changes in cells with RBP2 knockdown significantly overlap with gene expression changes in cells overexpressing pRB, consistent with the data that knockdown of RBP2 phenocopies reintroduction of pRB in SAOS-2 (RB-/-) cells Keywords: epistatic experiment

2008-08-29 | GSE9690 | GEO

RBP2 location analysis

Project description:RBP2 (JARID1A/RBBP2) enrichment at proximal promoter regions in differentiating promonocytic U937 cells and in the osteosarcoma SAOS-2 cells Keywords: differentiation treatment, ChIP-on-chip analysis

2008-08-29 | GSE10636 | GEO

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