TF Info Page for HNF4A (Nuclear receptor)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 1 Monomer or homomultimer High-throughput in vitro

Description

Description: hepatocyte nuclear factor 4 alpha [Source:HGNC Symbol;Acc:HGNC:5024]
Entrez Summary The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes. This gene may play a role in development of the liver, kidney, and intestines. Mutations in this gene have been associated with monogenic autosomal dominant non-insulin-dependent diabetes mellitus type I. Alternative splicing of this gene results in multiple transcript variants encoding several different isoforms. [provided by RefSeq, Apr 2012]
Ensembl ID: ENSG00000101076
External Link: CisBP
Interpro IPR000003; IPR000536; IPR001628; IPR001723; IPR003068; IPR008946;
Protein Domain: ENSP00000312987
Protein Domain: ENSP00000315180
Protein Domain: ENSP00000412111
Protein Domain: ENSP00000410911
Protein Domain: ENSP00000396216
Protein Domain: ENSP00000476310
Protein Domain: ENSP00000476609
Domain:
Protein: ENSP00000312987DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000315180DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000412111DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000410911DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000396216DBD: Nuclear Hormone ReceptorOther: Hormone_recep
Protein: ENSP00000476310DBD: Nuclear Hormone ReceptorOther:
Protein: ENSP00000476609DBD: Nuclear Hormone ReceptorOther: Hormone_recep

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:15581617
Vaquerizas 2009 TF classification
"a" Has direct evidence of TF function;
"b" Has evidence for an orthologous TF;
"c" contains likely DBDs, but has no functional evidence;
"x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription;
"other" category contains proteins without clear DBDs they curated from external sources.
a
CisBP considers it as a TF? Yes
TFclass considers it as a TF? Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding" Yes
GO-Info GO:0001077
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a
ISS - GO_REF:0000024
GO:0003700
sequence-specific DNA binding transcription factor activity
IDA - PMID:10330009, PMID:12911579, PMID:16488887,
GO:0003705
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity
IEA - GO_REF:0000019
GO:0004879
ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity
IEA - GO_REF:0000002
Initial Assessment
1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding;
1a2 There is high confidence data for a close ortholog (as defined in CisBP);
2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model;
2a2 There is lower confidence evidence for an close ortholog;
3a There is decent circumstantial evidence for its role as a TF or not;
4a Two or more datasets predict it as a TF;
5a One of the source datasets predicts is as a TF
1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source Annotation Motif Evidence
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
ChIP-seqmodENCODEDirect
ChIP-seqmodENCODEDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
MiscHOMERDirect
PBMBadis09Inferred - Hnf4a (100% AA Identity, Mus musculus)
SELEXJASPARInferred - Hnf4a (100% AA Identity, Mus musculus)
ChIP-seqJASPARInferred - HNF4G (92% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HNF4G (92% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HNF4G (92% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HNF4G (92% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HNF4G (92% AA Identity, Homo sapiens)
HT-SELEXNitta2015Inferred - Hnf4 (88% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Hnf4 (88% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Hnf4 (88% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Hnf4 (88% AA Identity, Drosophila melanogaster)

Structure

Structure PDB 3CBB

Experimental History

Method Constructs
Tried in PBM?
(Whether the protein was tried in PBM or not)
Tried in HT-SELEX
(Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information?
(Tried with another method and failed?)

External Contribution