P25490 (TYY1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transcriptional repressor protein YY1

Alternative name(s):
Delta transcription factor
INO80 complex subunit S
NF-E1
Yin and yang 1
Short name=YY-1

Gene names

Name:	YY1
Synonyms:	INO80S

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	414 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Multifunctional transcription factor that exhibits positive and negative control on a large number of cellular and viral genes by binding to sites overlapping the transcription start site. Binds to the consensus sequence 5'-CCGCCATNTT-3'; some genes have been shown to contain a longer binding motif allowing enhanced binding; the initial CG dinucleotide can be methylated greatly reducing the binding affinity. The effect on transcription regulation is depending upon the context in which it binds and diverse mechanisms of action include direct activation or repression, indirect activation or repression via cofactor recruitment, or activation or repression by disruption of binding sites or conformational DNA changes. Its activity is regulated by transcription factors and cytoplasmic proteins that have been shown to abrogate or completely inhibit YY1-mediated activation or repression. For example, it acts as a repressor in absence of adenovirus E1A protein but as an activator in its presence. May play an important role in development and differentiation. Proposed to recruit the PRC2/EED-EZH2 complex to target genes that are transcriptional repressed. Involved in DNA repair. In vitro, binds to DNA recombination intermediate structures (Holliday junctions). Ref.10 Ref.11 Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair; proposed to target the INO80 complex to YY1-responsive elements. Ref.10 Ref.11
Subunit structure	Interacts with YAF2 through the region encompassing the first and second zinc fingers. Component of the chromatin remodeling INO80 complex; specifically part of a complex module associated with the DBINO domain of INO80. Interacts with EED and EZH2; the interactions are indicative for an association with the PRC2/EED-EZH2 complex. Ref.6 Ref.8 Ref.10 Ref.11 Ref.13 Ref.19
Subcellular location	Nucleus matrix. Note: Associated with the nuclear matrix. Ref.5 Ref.11
Post-translational modification	Transiently poly-ADP-ribosylated by PARP1 upon DNA damage, with the effect of decreasing affinity of YY1 to its cognate DNA binding sites.
Sequence similarities	Belongs to the YY transcription factor family. Contains 4 C2H2-type zinc fingers.

Ontologies

Keywords
Biological process	DNA damage DNA recombination DNA repair Differentiation Spermatogenesis Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Polymorphism
Domain	Repeat Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Activator Repressor
PTM	ADP-ribosylation Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	RNA localization Inferred from electronic annotation. Source: Compara anterior/posterior pattern specification Inferred from electronic annotation. Source: Compara camera-type eye morphogenesis Inferred from electronic annotation. Source: Compara cell differentiation Inferred from electronic annotation. Source: UniProtKB-KW cellular response to UV Inferred from mutant phenotype Ref.11. Source: UniProtKB chromosome organization Inferred from electronic annotation. Source: Compara double-strand break repair via homologous recombination Inferred from mutant phenotype Ref.11. Source: UniProtKB response to UV-C Inferred from mutant phenotype Ref.11. Source: UniProtKB response to prostaglandin F stimulus Inferred from electronic annotation. Source: Compara spermatogenesis Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	Ino80 complex Inferred from direct assay Ref.11Ref.19. Source: UniProtKB PcG protein complex Inferred from electronic annotation. Source: Compara nuclear matrix Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane Inferred from direct assay. Source: HPA transcription factor complex Inferred from electronic annotation. Source: Compara
Molecular_function	RNA binding Inferred from direct assay PubMed 21729784. Source: MGI RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription Inferred from sequence or structural similarity. Source: BHF-UCL four-way junction DNA binding Inferred from direct assay Ref.11. Source: UniProtKB transcription coactivator activity Traceable author statement Ref.2. Source: ProtInc transcription corepressor activity Traceable author statement Ref.1. Source: ProtInc transcription regulatory region DNA binding Inferred from direct assay PubMed 9857059. Source: MGI zinc ion binding Traceable author statement Ref.1. Source: ProtInc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ACTL6A	O96019	5	EBI-765538,EBI-355018
ARRB1	P49407	4	EBI-765538,EBI-743313
INO80	Q9ULG1	5	EBI-765538,EBI-769345
PRKDC	P78527	2	EBI-765538,EBI-352053
RUVBL1	Q9Y265	4	EBI-765538,EBI-353675
RUVBL2	Q9Y230	5	EBI-765538,EBI-352939
Rybp	Q8CCI5	2	EBI-765538,EBI-929290	From a different organism.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 414

414

Transcriptional repressor protein YY1

PRO_0000047190

Regions

Zinc finger

296 – 320

25

C2H2-type 1

Zinc finger

325 – 347

23

C2H2-type 2

Zinc finger

353 – 377

25

C2H2-type 3

Zinc finger

383 – 407

25

C2H2-type 4

Region

257 – 341

85

Involved in nuclear matrix association

Region

333 – 371

39

Involved in repression of activated transcription

Region

371 – 397

27

Involved in masking transactivation domain

Compositional bias

43 – 53

11

Asp/Glu-rich (acidic)

Compositional bias

54 – 69

16

Gly-rich

Compositional bias

70 – 80

11

Poly-His

Compositional bias

159 – 170

12

Gly/Ser-rich

Sites

Metal binding

298

1

Zinc 1

Metal binding

303

1

Zinc 1

Metal binding

316

1

Zinc 1

Metal binding

320

1

Zinc 1

Metal binding

327

1

Zinc 2

Metal binding

330

1

Zinc 2

Metal binding

343

1

Zinc 2

Metal binding

347

1

Zinc 2

Metal binding

355

1

Zinc 3

Metal binding

360

1

Zinc 3

Metal binding

373

1

Zinc 3

Metal binding

377

1

Zinc 3

Metal binding

385

1

Zinc 4

Metal binding

390

1

Zinc 4

Metal binding

403

1

Zinc 4

Metal binding

407

1

Zinc 4

Amino acid modifications

Modified residue

118

1

Phosphoserine Ref.16 Ref.17 Ref.20

Modified residue

247

1

Phosphoserine Ref.12 Ref.14 Ref.16

Modified residue

378

1

Phosphothreonine Ref.14

Natural variations

Natural variant

380

1

D → Y De novo variant found in a patient with mental retardation. Ref.23

VAR_065086

Experimental info

Sequence conflict

65

1

H → R in AAA59926. Ref.2

Sequence conflict

196

1

G → R in AAA59467. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

414

Helix Strand Turn

Details...

Beta strand

306 – 309

4

Helix

310 – 317

8

Helix

318 – 320

3

Turn

328 – 330

3

Beta strand

333 – 336

4

Helix

337 – 343

7

Helix

344 – 346

3

Turn

358 – 360

3

Beta strand

363 – 365

3

Helix

367 – 378

12

Turn

397 – 400

4

Helix

401 – 407

7

Sequences

	Sequence		Length	Mass (Da)
	P25490 [UniParc]. Last modified December 15, 1998. Version 2. Checksum: 058C05A0AD2D04E6	FASTA	414	44,713
	10 20 30 40 50 60 MASGDTLYIA TDGSEMPAEI VELHEIEVET IPVETIETTV VGEEEEEDDD DEDGGGGDHG 70 80 90 100 110 120 GGGGHGHAGH HHHHHHHHHH PPMIALQPLV TDDPTQVHHH QEVILVQTRE EVVGGDDSDG 130 140 150 160 170 180 LRAEDGFEDQ ILIPVPAPAG GDDDYIEQTL VTVAAAGKSG GGGSSSSGGG RVKKGGGKKS 190 200 210 220 230 240 GKKSYLSGGA GAAGGGGADP GNKKWEQKQV QIKTLEGEFS VTMWSSDEKK DIDHETVVEE 250 260 270 280 290 300 QIIGENSPPD YSEYMTGKKL PPGGIPGIDL SDPKQLAEFA RMKPRKIKED DAPRTIACPH 310 320 330 340 350 360 KGCTKMFRDN SAMRKHLHTH GPRVHVCAEC GKAFVESSKL KRHQLVHTGE KPFQCTFEGC 370 380 390 400 410 GKRFSLDFNL RTHVRIHTGD RPYVCPFDGC NKKFAQSTNL KSHILTHAKA KNNQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Transcriptional repression by YY1, a human GLI-Kruppel-related protein, and relief of repression by adenovirus E1A protein." Shi Y., Seto E., Chang L.-S., Shenk T. Cell 67:377-388(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE.
[2]	"Isolation of a candidate repressor/activator, NF-E1 (YY-1, delta), that binds to the immunoglobulin kappa 3' enhancer and the immunoglobulin heavy-chain mu E1 site." Park K., Atchison M. Proc. Natl. Acad. Sci. U.S.A. 88:9804-9808(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Tissue: Foreskin.
[3]	Whitson R.H., Huang T., Dang J., Itakura K. Submitted (JUL-1992) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[4]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Brain and Lymph.
[5]	"Targeting of the YY1 transcription factor to the nucleolus and the nuclear matrix in situ: the C-terminus is a principal determinant for nuclear trafficking." McNeil S., Guo B., Stein J.L., Lian J.B., Bushmeyer S., Seto E., Atchison M.L., Penman S., van Wijnen A.J., Stein G.S. J. Cell. Biochem. 68:500-510(1998) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[6]	"Yeast two-hybrid cloning of a novel zinc finger protein that interacts with the multifunctional transcription factor YY1." Kalenik J.L., Chen D., Bradley M.E., Chen S.-J., Lee T.-C. Nucleic Acids Res. 25:843-849(1997) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH YAF2.
[7]	"Poly(ADP-ribosyl)ation of transcription factor Yin Yang 1 under conditions of DNA damage." Oei S.L., Shi Y. Biochem. Biophys. Res. Commun. 285:27-31(2001) [PubMed] [Europe PMC] [Abstract] Cited for: POLY-ADP-RIBOSYLATION BY PARP1.
[8]	"The polycomb group protein EED interacts with YY1, and both proteins induce neural tissue in Xenopus embryos." Satijn D.P.E., Hamer K.M., den Blaauwen J., Otte A.P. Mol. Cell. Biol. 21:1360-1369(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH EZH2 AND EZH2.
[9]	"Transcription factor YY1: structure, function, and therapeutic implications in cancer biology." Gordon S., Akopyan G., Garban H., Bonavida B. Oncogene 25:1125-1142(2006) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW ON FUNCTION.
[10]	"YY1 functions with INO80 to activate transcription." Cai Y., Jin J., Yao T., Gottschalk A.J., Swanson S.K., Wu S., Shi Y., Washburn M.P., Florens L., Conaway R.C., Conaway J.W. Nat. Struct. Mol. Biol. 14:872-874(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE INO80 COMPLEX.
[11]	"A YY1-INO80 complex regulates genomic stability through homologous recombination-based repair." Wu S., Shi Y., Mulligan P., Gay F., Landry J., Liu H., Lu J., Qi H.H., Wang W., Nickoloff J.A., Wu C., Shi Y. Nat. Struct. Mol. Biol. 14:1165-1172(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN DNA REPAIR, SUBCELLULAR LOCATION, DNA-BINDING, PROTEIN INTERACTION, IDENTIFICATION IN THE INO80 COMPLEX.
[12]	"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle." Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M. Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-247, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[13]	"Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and in the Ino80 chromatin-remodeling complex." Yao T., Song L., Jin J., Cai Y., Takahashi H., Swanson S.K., Washburn M.P., Florens L., Conaway R.C., Cohen R.E., Conaway J.W. Mol. Cell 31:909-917(2008) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE INO80 COMPLEX, MASS SPECTROMETRY.
[14]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-247 AND THR-378, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[15]	"YY1's longer DNA-binding motifs." Kim J., Kim J. Genomics 93:152-158(2009) [PubMed] [Europe PMC] [Abstract] Cited for: DNA-BINDING MOTIF.
[16]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-118 AND SER-247, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[17]	"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-118, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[18]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[19]	"Subunit organization of the human INO80 chromatin remodeling complex: An evolutionarily conserved core complex catalyzes ATP-dependent nucleosome remodeling." Chen L., Cai Y., Jin J., Florens L., Swanson S.K., Washburn M.P., Conaway J.W., Conaway R.C. J. Biol. Chem. 286:11283-11289(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE INO80 COMPLEX.
[20]	"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation." Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B. Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-118, MASS SPECTROMETRY.
[21]	"Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator." Houbaviy H.B., Usheva A., Shenk T., Burley S.K. Proc. Natl. Acad. Sci. U.S.A. 93:13577-13582(1996) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 304-414.
[22]	"Design, synthesis and structure of a zinc finger with an artificial beta-turn." Viles J.H., Patel S.U., Mitchell J.B.O., Moody C.M., Justice D.E., Uppenbrink J., Doyle P.M., Harris C.J., Sadler P.J., Thornton J.M. J. Mol. Biol. 279:973-986(1998) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 353-379.
[23]	"A de novo paradigm for mental retardation." Vissers L.E., de Ligt J., Gilissen C., Janssen I., Steehouwer M., de Vries P., van Lier B., Arts P., Wieskamp N., del Rosario M., van Bon B.W., Hoischen A., de Vries B.B., Brunner H.G., Veltman J.A. Nat. Genet. 42:1109-1112(2010) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT TYR-380.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M77698 mRNA. Translation: AAA59467.1.
M76541 mRNA. Translation: AAA59926.1.
Z14077 mRNA. Translation: CAA78455.1.
BC037308 mRNA. Translation: AAH37308.1.
BC065366 mRNA. Translation: AAH65366.1.

IPI

IPI00014513.

PIR

A40350.

RefSeq

NP_003394.1. NM_003403.4.

UniGene

Hs.388927.
Hs.603118.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1UBD	X-ray	2.50	C	293-414	[»]
1ZNM	NMR	-	A	352-379	[»]

ProteinModelPortal

P25490.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-150N.
DIP-28144N.

IntAct

P25490. 25 interactions.

STRING

9606.ENSP00000262238.

PTM databases

PhosphoSite

P25490.

Polymorphism databases

DMDM

3915889.

Proteomic databases

PaxDb

P25490.

PeptideAtlas

P25490.

PRIDE

P25490.

Protocols and materials databases

DNASU

7528.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000262238; ENSP00000262238; ENSG00000100811.

GeneID

7528.

KEGG

hsa:7528.

UCSC

uc001ygy.1. human.

Organism-specific databases

CTD

7528.

GeneCards

GC14P101071.

HGNC

HGNC:12856. YY1.

HPA

CAB009392.
HPA001119.

MIM

600013. gene.

neXtProt

NX_P25490.

PharmGKB

PA37445.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG5048.

HOGENOM

HOG000008232.

HOVERGEN

HBG006823.

InParanoid

P25490.

KO

K09201.

OMA

DIDHESV.

OrthoDB

EOG4D26QN.

PhylomeDB

P25490.

Enzyme and pathway databases

Pathway_Interaction_DB

hdac_classi_pathway. Signaling events mediated by HDAC Class I.

Gene expression databases

ArrayExpress

P25490.

Bgee

P25490.

CleanEx

HS_YY1.

Genevestigator

P25490.

GermOnline

ENSG00000100811. Homo sapiens.

Family and domain databases

Gene3D

3.30.160.60. 4 hits.

InterPro

IPR017114. TF_Yin_yang.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]

Pfam

PF00096. zf-C2H2. 1 hit.
[Graphical view]

PIRSF

PIRSF037113. TF_Yin_yang. 1 hit.

SMART

SM00355. ZnF_C2H2. 4 hits.
[Graphical view]

PROSITE

PS00028. ZINC_FINGER_C2H2_1. 4 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

YY1. human.

EvolutionaryTrace

P25490.

GenomeRNAi

7528.

NextBio

29449.

PMAP-CutDB

P25490.

SOURCE

Search...

Entry information

Entry name

TYY1_HUMAN

Accession

Primary (citable) accession number: P25490
Secondary accession number(s): Q14935

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	December 15, 1998
Last modified:	May 1, 2013
This is version 154 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.