nuclear factor of kappa light polypeptide gene enhancer in B-cells 1
PDB ID : 1MDI
|Protein Family||p53-like transcription factors|
|Type||Pol II TF|
NF-kB (nuclear factor kappa B) is a pleiotropic transcription factor present in all cell types. It is activated by many different stimuli (cytokines, oxidant-free radicals, ultraviolet irradiation, and bacterial or viral products for example) and is involved in several biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis, and apoptosis. NF-kB is a homo- or heterodimeric complex formed by the REL-like domain-containing proteins such as RELA, RELB, NF-kB1. The RELA/NF-kB1 heterodimeric complex is the best studied one. Different dimer combinations act as transcriptional activators or repressors. NF-kB is a 105kD protein which can undergo cotranslational processing by the 26S proteasome to produce a 50kD protein. The 105kD protein is a REL-specific transcription inhibitor and the 50kD protein is a DNA-binding subunit of the NF-kB protein complex. NF-kB complexes are held in the cytoplasm in an inactive state by a protein complex called inhibitor of kappa B (IkB). IkB inactivates NF-kB by masking its nuclear localization signals. Activation (and nuclear translocation) of NF-kB occurs via degradation of IkB, a process that is initiated by phosphorylation of IkB by IkB kinase (IKK). NF-kB turns on expression of IkB forming a negative feedback loop. Inappropriate activation of NF-kB has been associated with a number of inflammatory diseases while persistent inhibition of NF-kB leads to inappropriate immune cell development or delayed cell growth.
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:Stanford Protocol:IgG-rab Treatment:None Antibody:NFKB