retinoid X receptor, alpha
PDB ID : 1DSZ
|Protein Family||Glucocorticoid receptor-like (DNA-binding domain)|
|Type||Pol II TF|
RXRA (retinoid X receptor alpha) is a member of the retinoid X receptor (RXR) and retinoic acid receptor (RAR) steroid and thyroid hormone nuclear receptor superfamily of transcriptional regulators. There are three RXR subtypes: RXRalpha (expressed in the liver, kidneys, epidermis, and intestines); RXRbeta (widely distributed); and RXRgamma (restricted to muscle, the pituitary gland, and certain parts of the brain). RAR/RXR heterodimers bind to the retinoic acid response element (RARE) in the promoter region of target genes, which is composed of tandem 5'-AGGTCA-3' sites. In the absence of ligand, RXR-RAR heterodimers associate with a multiprotein complex containing transcriptional corepressors that induce chromatin condensation. On ligand binding, the corepressors dissociate, and the RXR-RAR heterodimers associate with transcriptional coactivators. Common binding partners for RXR-RAR include PPARA (for transcriptional activity on fatty acid oxidation genes such as ACOX1 and the P450 system genes), liver X receptors, and vitamin D receptors.
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:GM12878 Lab:HudsonAlpha Protocol:PCR1x Treatment:None Antibody:RXRA