IRF6

interferon regulatory factor 6 | OFC6, VWS1, LPS, VWS

This gene encodes a member of the interferon regulatory transcription factor (IRF) family. Family members share a highly-conserved N-terminal helix-turn-helix DNA-binding domain and a less conserved C-terminal protein-binding domain. The encoded protein may be a transcriptional activator. Mutations in this gene can cause van der Woude syndrome and popliteal pterygium syndrome. Mutations in this gene are also associated with non-syndromic orofacial cleft type 6. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2011]

Biological processes 31 terms

DNA binding (GO:0003677)DNA binding (GO:0003677)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)apical part of cell (GO:0045177)chromatin (GO:0000785)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)extracellular exosome (GO:0070062)immune system process (GO:0002376)mammary gland epithelial cell differentiation (GO:0060644)mammary gland epithelial cell differentiation (GO:0060644)negative regulation of cell population proliferation (GO:0008285)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific DNA binding (GO:0043565)sequence-specific double-stranded DNA binding (GO:1990837)transcription cis-regulatory region binding (GO:0000976)

Expression (TPM)

TFs regulating IRF6 0 TFs

Transcription factors with Perturb-seq knockdown data for IRF6. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = IRF6 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to IRF6

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of IRF6, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr1:209,565,881–209,566,600	239.9 kb	Distal (>10kb) Multiome	193
chr1:209,627,346–209,628,178	178.4 kb	Distal (>10kb) Multiome	368
chr1:209,747,459–209,748,502	58.3 kb	Distal (>10kb) Multiome	723
chr1:209,784,214–209,785,171	21.6 kb	Distal (>10kb) Multiome	859
chr1:209,805,245–209,806,661	5 bp	At TSS Multiome	472
chr1:209,827,579–209,828,429	21.8 kb	Distal (>10kb) Multiome	833
chr1:209,888,562–209,889,538	82.7 kb	Distal (>10kb) Multiome	75
chr1:209,937,461–209,938,825	131.9 kb	Distal (>10kb) Multiome	555

Genome Browser

Genomic view of the IRF6 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.