Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Brg1 Modulates Enhancer Activation and Polycomb-mediated Repression in Mesoderm Differentiation [ChIP-exo]

ABSTRACT: We investigated the genome-wide occupancy changes in normal and Brg1-deleted mesoderm differentiation of mouse embryonic stem cells of chromatin regulators and histone modifications. ChIP exo for BRG1 in 2 conditions: Day4 THF (Control) and Day4 4OHT (Brg1-deleted). 1-2 replicates per condition.

ORGANISM(S): Mus musculus

SUBMITTER: Jeffrey Alexander

PROVIDER: E-GEOD-63976 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Brg1 modulates enhancer activation in mesoderm lineage commitment.

Alexander Jeffrey M JM Hota Swetansu K SK He Daniel D Thomas Sean S Ho Lena L Pennacchio Len A LA Bruneau Benoit G BG

Development (Cambridge, England) 20150326 8

The interplay between different levels of gene regulation in modulating developmental transcriptional programs, such as histone modifications and chromatin remodeling, is not well understood. Here, we show that the chromatin remodeling factor Brg1 is required for enhancer activation in mesoderm induction. In an embryonic stem cell-based directed differentiation assay, the absence of Brg1 results in a failure of cardiomyocyte differentiation and broad deregulation of lineage-specific gene express ...[more]

PMID: 25813539

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Project description:BRG1, an ATPase catalytic subunit of the SWI/SNF chromatin remodeling complex, has been identified as a tumor suppressor protein, as it has been shown to play a role in Nucleotide Excision Repair (NER) of CPDs, suppress apoptosis, and restore checkpoint deficiency, in response to UV exposure. Although BRG1 has been shown to regulate transcription of some genes that are instrumental in proper DNA damage repair and cell cycle maintenance in response to UV, its role in transcriptional regulation of the whole genome in response to UV has not yet been elucidated. With whole genome expression profiling in SW13 cells, we show that upon UV induction, BRG1 regulates transcriptional expression of many genes involved in cell stress response. Additionally, our results also highlight BRG1’s general role as a master regulator of the genome, as it transcriptionally regulates approximately 4.8% of the human genome, including expression of genes involved in many pathways. SW13 cells without or with BRG1 protein exrpession were treated with UV-C (10 J/m2) or mock treated. Cells were incubated for 6 hrs after UV or mock treaments, total RNA was prepared using TRIZOL reagent (Invitrogen, Carlsbad, CA), followed by the RNeasy kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. Three independent biological replicates of SW13+pREP7 and SW13+pREP7+BRG1 were subjected to microarray analysis using Affymetrix U133 plus 2.0 gene chip. Target synthesis and GeneChip hybridization, washing, staining, and scanning were performed at the Molecular Biology Core at Washington State University. Microarray output was examined visually for excessive background noise and physical anomalies. The default MAS statistical values were used for all analyses. All probe sets on each array were scaled to a mean target signal intensity of 125, with the signal correlating to the amount of transcript in the sample. An absolute analysis using MAS was performed to assess the relative abundance of the 47,000 represented transcripts and variants, including 38,500 human genes, based on signal and detection

Dataset Information

Brg1 Modulates Enhancer Activation and Polycomb-mediated Repression in Mesoderm Differentiation [ChIP-exo]

Publications

Brg1 modulates enhancer activation in mesoderm lineage commitment.

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