E2F transcription factor 4, p107/p130-binding
PDB ID : 1CF7
|Protein Family||Winged helix DNA-binding domain|
|Type||Pol II TF|
E2F4 is a member of the E2F family of transcription factors which play a crucial role in controlling the cell cycle, action of tumor suppressor proteins, and are a target of the transforming proteins of small DNA tumor viruses. E2F proteins contain several evolutionally conserved domains found in most members of the family, including a DNA binding domain, a dimerization domain (which determines interaction with the differentiation-regulated transcription factor proteins (DP)), a transactivation domain enriched in acidic residues, and a tumor suppressor protein association domain embedded within the transactivation domain. E2F4 is a transcriptional inhibitor that binds DNA cooperatively with DP proteins through the E2 recognition site 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. It plays an important role in the suppression of proliferation-associated genes, and binds to the tumor suppressor proteins p130, p107, and pRb, as well as RBL1, RBL2, and SMAD3. E2F4 mutations and increased expression may be associated with human cancer.
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:USC Protocol:std Treatment:None Antibody:E2F4