The Human Transcription Factors

Conclusion

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

Description

Description:

YY1 transcription factor [Source:HGNC Symbol;Acc:HGNC:12856]

Entrez Summary

microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

Ensembl ID:

ENSG00000100811

External Link:

CisBP

Interpro

IPR007087; IPR015880; IPR017114; ;

Protein Domain:

ENSP00000262238

Protein Domain:

ENSP00000452140

Protein Domain:

ENSP00000451329

Protein Domain:

ENSP00000452225

Domain:

Protein: ENSP00000262238	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000452140	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000451329	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000452225	DBD: C2H2 ZF Containing Proteins	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:12584314 7501456 9141463 10452940 7565750 15316102 1655281 1720509
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:0001078 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 TAS - PMID:1946405
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
SMiLE-seq	Isakova2017		Direct
HT-SELEX	Jolma2013		Direct
RCADE	Schmitges2016		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	JASPAR		Direct
ChIP-seq	Najafabadi2015		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
Transfac	Transfac	License required	Inferred - TYY2_RAT (89% AA Identity, Rattus norvegicus)
HT-SELEX	Yin2017		Inferred - YY2 (81% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - YY2 (81% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - ZFP42 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - ZFP42 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - ZFP42 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - Zfp42 (70% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Zfp42 (70% AA Identity, Mus musculus)

Structure

Structure	PDB	1UBD

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

Name
Email
Comment
Reference

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The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 298, "scoreName": "E-value", "accession": "PF00096.24", "start": 297, "score": 1.8e-17, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 320}}, {"startStyle": "curved", "end": 347, "endStyle": "curved", "aliStart": 325, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 347, "start": 325, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 347, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 325, "scoreName": "E-value", "accession": "PF00096.24", "start": 325, "score": 1.8e-17, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 347}}, {"startStyle": "curved", "end": 377, "endStyle": "curved", "aliStart": 353, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 377, "start": 353, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 377, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 353, "scoreName": "E-value", "accession": "PF00096.24", "start": 353, "score": 1.8e-17, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 377}}, {"startStyle": "curved", "end": 407, "endStyle": "curved", "aliStart": 383, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 407, "start": 383, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 407, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 383, "scoreName": "E-value", "accession": "PF00096.24", "start": 383, "score": 1.8e-17, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 407}}], "length": 415}

{"regions": [{"startStyle": "curved", "end": 153, "endStyle": "curved", "aliStart": 129, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 153, "start": 129, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 153, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 129, "scoreName": "E-value", "accession": "PF00096.24", "start": 129, "score": 9.7e-10, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 153}}, {"startStyle": "curved", "end": 183, "endStyle": "curved", "aliStart": 159, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 183, "start": 159, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 183, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 159, "scoreName": "E-value", "accession": "PF00096.24", "start": 159, "score": 9.7e-10, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 183}}], "length": 191}

TF Info Page for YY1 (C2H2 ZF(non-KRAB))

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution