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forkhead box A1
PDBsearch FOXA1
HGNC(alias)FOXA1 (HNF3A)
Gene CardFOXA1
UCSCBrowser view
Protein FamilyWinged helix DNA-binding domain
TypePol II TF
Ensembl Exp.Human


FOXA1 is a member of the forkhead class of DNA-binding proteins, and binds to the consensus sequence 5'-[AC]A[AT]T[AG]TT[GT][AG][CT]T[CT]-3'. It is a hepatocyte nuclear factor that serves as a transcriptional activator for liver-specific transcripts such as albumin and transthyretin. FOXA1 is involved in embryonic development, establishment of tissue-specific gene expression, and regulation of gene expression in differentiated tissues. It is thought to help open compacted chromatin through interactions with nucleosomal core histones, and play a role in translating epigenetic signatures into cell type-specific enhancer-driven transcriptional programs. Its differential recruitment to chromatin is dependent on distribution of histone H3K4 methylation in estrogen-regulated genes. FOXA1 also plays several other roles. It is required for ESR1 binding to the NKX2-1 promoter in breast cancer cells; it binds to the RPRM promoter and is required for estrogen-induced repression of RPRM; it is involved in regulation of apoptosis (by inhibiting the expression of BCL2); and it helps regulate the cell cycle by activating expression of CDKN1B (alone or in conjunction with BRCA1).

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.

ECC-1 1
HepG2 2
T-47D 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

No Available Data

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:HepG2   Lab:HudsonAlpha   Protocol:v041610.1   Treatment:None   Antibody:FOXA1_(SC-101058)   

Binding of Other Transcription Factors or Histone Marks at the FOXA1 Peaks

Select HeatmapLab:   Cellline:  

  • Comparison with the FOXA1 peaks in A549 cells generated by HAIB

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