INI1

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SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
INI1
PDBsearch INI1
HGNC(alias)SMARCB1 (BAF47,INI1,hSNFS,SNF5L1,Snr1,RDT,Sfh1p,Ini1)
Gene CardSMARCB1
Entrez6598
RefSeqNM_001007468
UniProtQ12824
UCSCBrowser view
WikipediaSMARCB1
Protein FamilyUnknown
TypeATP-dependent chromatin complexes
Ensembl Exp.Human

Function

INI1 (also known as BAF47 and SMARCB1) is a core component of the ATP-dependent BAF (hSWI/SNF) chromatin-remodeling complex. The BAF complex plays an important role in cell proliferation and differentiation, antiviral activities, and inhibition of tumor formation. INI1 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. INI1 also is associated with activation of the CSF1 promoter, vitamin D-coupled transcription regulation (via its association with the WINAC complex), and may bind to and enhance the DNA joining activity of HIV-1 integrase. It is a tumor suppressor, and INI1 mutations are associated with malignant rhabdoid tumors. Two 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.

+/-
Stanford
HeLa-S3 1
K562 1


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.

Select MotifCell Line:   Lab:   Protocol:   Treatment:   Antibody:  

Cell Line:HeLa-S3   Lab:Stanford   Protocol:IgG-mus   Treatment:None   Antibody:Ini1   

Binding of Other Transcription Factors or Histone Marks at the INI1 Peaks

Select HeatmapLab:   Cellline:  

  • Comparison with the INI1 peaks in HELAS3 cells generated by SYDH

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