SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
PDB ID : 2H60
|Protein Family||BRK domain-like|
|Type||ATP-dependent chromatin complexes|
BRG1 (also known as SMARCA4) is a member of the SWI/SNF family of proteins which have helicase and ATPase activities, and are involved in chromatin-remodeling. It belongs to the neural progenitor-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development, a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and commit to their adult state. This transition requires a switch in subunit composition of the npBAF and nBAF complexes. The npBAF complex is essential for the self-renewal/proliferative capacity of multipotent neural stem cells, and works with CREST to regulate the activity of genes essential for dendrite growth. The CREST-BRG1 complex is a multiprotein complex that regulates promoter activation via a calcium-dependent release of a repressor complex and recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which releases the repressor complex and recruits CREBBP to the promoter by a CREST-dependent mechanism, leading to transcriptional activation. BRG1 also is involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, acts as a corepressor of ZEB1 to regulate E-cadherin transcription, and is required for induction of epithelial-mesenchymal transition (EMT) by ZEB1. In addition, BRG1 can bind BRCA1, as well as regulate the expression of the tumorigenic protein CD44. Multiple transcript variants encoding different isoforms have been found for this gene.
ENCODE ChIP-seq Datasets
Indicated in the matrix are the numbers of datasets specified by lab and cell line; when the number is greater than 1, multiple ChIP-seq experiments have been performed, some upon treatments. Click the numbers to download the data files on ChIP-seq peaks, alignments, etc.
Average Profiles of Modified Histones around the Summit of ChIP-seq Peaks
Average histone modification profiles are shown for the [-2 kb, +2 kb] window around the summits of TF ChIP-seq peaks, separately for peaks that are proximal ([-1kb, +1kb]) to an annotated transcript (dashed lines) start sites and for peaks that are distal (more than 1kb) to all annotated transcripts (solid lines) start sites. Proximal profiles are arranged such that the transcriptional direction of the nearest transcript is toward the right. Histone modification data were generated by the Broad team, using antibodies to pull down modified histones followed by deep sequencing of the genomic DNA associated with the modified histones. Only histone modification data from the same cell line as the TF ChIP-seq data are shown.
Mouse over a curve to reveal its identity. Mouse over a histone modification in the legend to show its curves and gray out other histone modifications in the figures. Click a histone modification in the legend to toggle on/off its curve in all figures. Click the “Proximal” or “Distal” button in the legend to show only the average histone modification profiles anchored around ChIP-seq peaks that are proximal or distal to annotated transcripts.
Average Profiles of Nucleosomes around the Summit of ChIP-seq Peaks
Average nucleosome occupancy profiles are shown for the [-2 kb, +2 kb] window around the summits of TF ChIP-seq peaks, separately for peaks that are proximal to an annotated transcript (red lines) and for peaks that are distal to all annotated transcripts (blue lines), as defined in the previous section. Nucleosome positioning data in GM12878 and K562 were generated by the Stanford team, with micrococcal nuclease digestion of chromatin followed by deep sequencing of mononucleosomal DNA.
Motifs Enriched in the Top 500 ChIP-seq Peaks
The sequences of the top 500 TF ChIP-seq peaks were used to identify enriched motifs de novo, using the MEME-ChIP suite of tools. Five motifs are reported (M1 to M5), with motif name, sequence logo, and number of peaks out of the top 500 peaks that contain a site for the motif. The motifs are then used to scan the entire set of ChIP-seq peaks and the two flanking (control) regions using the FIMO tool, and two quantities are reported for bins of peaks sorted by their ChIP-seq q-values: percentage of the peaks that contain a site for the motif, and the distribution of the distances of the motif site to the summit of the peak.
Cell Line:HeLa-S3 Lab:Yale Protocol:IgG-mus Treatment:None Antibody:Brg1