TAF1

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TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa
TAF1

PDB ID : 1EQF
PDB1EQF 3AAD
HGNC(alias)TAF1 (TAFII250,KAT4,DYT3,BA2R,NSCL2,TAF2A,CCG1,CCGS,DYT3/TAF1)
Gene CardTAF1
Entrez6872
RefSeqNM_004606
UniProtP21675
UCSCBrowser view
WikipediaTAF1
Protein FamilyTAF(II)230 TBP-binding fragment
Typegeneral Pol II associated factor, not site-specific
Ensembl Exp.Human

Function

TAF1 (TATA box binding protein-associated factor 1, also known as TAF250) is the largest subunit and core scaffold of the TFIID complex. TFIID binds the core promoter to properly position RNA polymerase II, and serves as the scaffold for assembly of the remainder of the transcription complex. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors to facilitate complex assembly and transcription initiation. TAF1 binds to core promoter sequences encompassing the transcription start site. It also binds to activators and other transcriptional regulators, and these interactions affect the rate of transcription initiation. TAF1 contains two independent protein kinase domains at the N and C-termini, but also can act as an acetyltransferase and a ubiquitin-activating/conjugating enzyme. TAF1 is part of a complex transcriptional unit (TAF1/DYT3), wherein some products share exons with TAF1 as well as additional exons downstream.

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.

+/-
HudsonAlpha
A549 1
GM12878 1
GM12891 1
GM12892 1
H1-hESC 1
HeLa-S3 1
HepG2 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:GM12878   Lab:HudsonAlpha   Protocol:PCR1x   Treatment:None   Antibody:TAF1   

Binding of Other Transcription Factors or Histone Marks at the TAF1 Peaks

Select HeatmapLab:   Cellline:  

  • Comparison with the TAF1 peaks in A549 cells generated by HAIB