Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of BRG1 response genes in human SW13 cells

ABSTRACT: BRG1 response genes in SW13 cells

ORGANISM(S): Homo sapiens

SUBMITTER: Xin Chen

PROVIDER: E-SMDB-2974 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Regulation of CSF1 promoter by the SWI/SNF-like BAF complex.

Liu R R Liu H H Chen X X Kirby M M Brown P O PO Zhao K K

Cell 20010801 3

The mammalian BAF complex regulates gene expression by modifying chromatin structure. In this report, we identify 80 genes activated and 2 genes repressed by the BAF complex in SW-13 cells. We find that prior binding of NFI/CTF to the NFI/CTF binding site in CSF1 promoter is required for the recruitment of the BAF complex and the BAF-dependent activation of the promoter. Furthermore, the activation of the CSF1 promoter requires Z-DNA-forming sequences that are converted to Z-DNA structure upon a ...[more]

PMID: 11509180

Similar Datasets

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

Transcription profiling of BRG1 response genes in human SW13 cells

Publications

Regulation of CSF1 promoter by the SWI/SNF-like BAF complex.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets