SETDB1

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SET domain, bifurcated 1
SETDB1

PDB ID : 3DLM
PDB3DLM
HGNC(alias)SETDB1 (ESET,KMT1E,KIAA0067,KG1T)
Gene CardSETDB1
Entrez9869
RefSeqNM_001145415
UniProtQ15047
UCSCBrowser view
WikipediaSETDB1
Protein FamilyDNA-binding domain
Typehistone methylation complexes
Ensembl Exp.Human

Function

SETDB1 (SET domain, bifurcated 1) is an H3K9-selective histone methyltransferase. TRIM28/TIF1B (a factor recruited by KRAB zinc-finger proteins) targets SETDB1 to histone H3. H3K9 trimethylation (H3K9me3) is a specific tag for epigenetic transcriptional repression, and functions by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. It functions in euchromatin regions, and plays a central role in the silencing of euchromatic genes. SETDB1 likely forms a complex with MBD1 and ATF7IP to repress transcription and couple DNA methylation to H3K9me3. Its activity is dependent on MBD1 and is heritably maintained through DNA replication by being recruited by CAF-1.

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.

+/-
USC
K562 2
U2OS 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:K562   Lab:USC   Protocol:UCDavis   Treatment:MNaseD   Antibody:SETDB1   

Binding of Other Transcription Factors or Histone Marks at the SETDB1 Peaks

Select HeatmapLab:   Cellline:  

  • Comparison with the SETDB1 peaks in K562 cells generated by SYDH

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