tripartite motif containing 28
PDB ID : 1FP0
|Protein Family||FYVE/PHD zinc finger|
|Type||histone methylation complexes|
KAP1 (KRAB associated protein 1, also known as TRIM28) is a member of the tripartite motif family which includes three zinc-binding domains: a RING, B-box types 1 and 2, and a coiled-coil region. It mediates transcriptional repression by interacting with the Kruppel-associated box (KRAB) repression domain found in many transcription factors. KAP1 mediates gene silencing by recruiting CHD3 (a subunit of the nucleosome remodeling and deacetylation (NuRD) complex) and SETDB1 (an H3K9 methylase) to the promoter regions of KRAB target genes. It enhances transcriptional repression by coordinating H3K9 methylation, H3K9 and H3K14 deacetylation, and the disposition of HP1 proteins to silence gene expression. KAP1 is a corepressor for ERBB4, and may play a role as a coactivator for CEBPB and NR3C1 in the transcriptional activation of ORM1. It inhibits E2F1 activity by preventing E2F1 acetylation and promoting formation of an E2F1-HDAC1 complex. In the absence of RB1, KAP1 may act as a partial backup to prevent E2F1-mediated apoptosis. It also is known to be an important regulator of CDKN1A/p21(CIP1).
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:K562 Lab:USC Protocol:UCDavis Treatment:None Antibody:KAP1