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Protein

Core histone macro-H2A.1

Gene

H2afy

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Variant histone H2A which replaces conventional H2A in a subset of nucleosomes where it represses transcription. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Involved in stable X chromosome inactivation. Inhibits the binding of transcription factors and interferes with the activity of remodeling SWI/SNF complexes. Inhibits histone acetylation by EP300 and recruits class I HDACs, which induces a hypoacetylated state of chromatin. In addition, isoform 1, but not isoform 2, binds ADP-ribose and O-acetyl-ADP-ribose, and may be involved in ADP-ribose-mediated chromatin modulation.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiREACT_264471. NoRC negatively regulates rRNA expression.
REACT_27235. Meiotic Recombination.
REACT_287050. Meiotic synapsis.
REACT_326896. NoRC negatively regulates rRNA expression.
REACT_351456. DNA methylation.
REACT_75800. Meiotic Synapsis.

Names & Taxonomyi

Protein namesi
Recommended name:
Core histone macro-H2A.1
Short name:
Histone macroH2A1
Short name:
mH2A1
Alternative name(s):
H2A.y
H2A/y
Gene namesi
Name:H2afy
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:1349392. H2afy.

Subcellular locationi

  • Nucleus
  • Chromosome

  • Note: Enriched in inactive X chromosome chromatin and in senescence-associated heterochromatin. In quiescent lymphocytes, associated with centromeric constitutive heterochromatin.

GO - Cellular componenti

  • Barr body Source: MGI
  • centrosome Source: MGI
  • condensed chromosome Source: MGI
  • ESC/E(Z) complex Source: Ensembl
  • extracellular exosome Source: MGI
  • nuclear chromatin Source: MGI
  • nuclear chromosome Source: MGI
  • nucleolus Source: MGI
  • nucleoplasm Source: MGI
  • nucleosome Source: UniProtKB-KW
  • nucleus Source: MGI
  • pericentric heterochromatin Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 372372Core histone macro-H2A.1PRO_0000227904Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei18 – 181N6-methyllysineBy similarity
Modified residuei116 – 1161N6-acetyllysine; alternate1 Publication
Cross-linki116 – 116Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternateBy similarity
Cross-linki117 – 117Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei123 – 1231N6-acetyllysine1 Publication
Modified residuei129 – 1291Phosphothreonine1 Publication
Modified residuei170 – 1701PhosphoserineBy similarity
Modified residuei173 – 1731PhosphoserineBy similarity
Modified residuei178 – 1781PhosphothreonineBy similarity

Post-translational modificationi

Monoubiquitinated at either Lys-116 or Lys-117. May also be polyubiquitinated. Ubiquitination is mediated by the CUL3/SPOP E3 complex and does not promote proteasomal degradation. Instead, it is required for enrichment in inactive X chromosome chromatin (By similarity).By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ9QZQ8.
PaxDbiQ9QZQ8.
PRIDEiQ9QZQ8.

PTM databases

PhosphoSiteiQ9QZQ8.

Expressioni

Tissue specificityi

Ubiquitously expressed, with high levels in testis. Present in liver, kidney and adrenal gland (at protein level). In the liver, present in hepatocytes and at a lesser extent in cells of the bile ducts. In the kidney, present in proximal and distal convoluted tubules and in straight proximal tubules. In the adrenal gland, present in inner cells of the cortex and medulla.2 Publications

Gene expression databases

BgeeiQ9QZQ8.
CleanExiMM_H2AFY.
ExpressionAtlasiQ9QZQ8. baseline and differential.
GenevestigatoriQ9QZQ8.

Interactioni

Subunit structurei

The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. Interacts with SPOP. Part of a complex consisting of H2AFY, CUL3 and SPOP. Interacts with HDAC1 and HDAC2 (By similarity).By similarity

Protein-protein interaction databases

BioGridi205061. 1 interaction.
IntActiQ9QZQ8. 3 interactions.
MINTiMINT-4121159.

Structurei

3D structure databases

ProteinModelPortaliQ9QZQ8.
SMRiQ9QZQ8. Positions 10-117, 181-369.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 117116Histone H2AAdd
BLAST
Domaini184 – 370187MacroPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi116 – 16146Lys-richAdd
BLAST

Sequence similaritiesi

Contains 1 histone H2A domain.Curated
Contains 1 Macro domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG2110.
GeneTreeiENSGT00760000119217.
HOGENOMiHOG000234653.
HOVERGENiHBG009342.
InParanoidiQ9QZQ8.
KOiK11251.
OMAiQVVQADI.
OrthoDBiEOG71G9VP.
PhylomeDBiQ9QZQ8.
TreeFamiTF332276.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR021171. Core_histone_macro-H2A.
IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
IPR002589. Macro_dom.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF01661. Macro. 1 hit.
[Graphical view]
PIRSFiPIRSF037942. Core_histone_macro-H2A. 1 hit.
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00506. A1pp. 1 hit.
SM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS51154. MACRO. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 2 (identifier: Q9QZQ8-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSSRGGKKKS TKTSRSAKAG VIFPVGRMLR YIKKGHPKYR IGVGAPVYMA
60 70 80 90 100
AVLEYLTAEI LELAGNAARD NKKGRVTPRH ILLAVANDEE LNQLLKGVTI
110 120 130 140 150
ASGGVLPNIH PELLAKKRGS KGKLEAIITP PPAKKAKSPS QKKPVAKKTG
160 170 180 190 200
GKKGARKSKK KQGEVSKAAS ADSTTEGTPT DGFTVLSTKS LFLGQKLNLI
210 220 230 240 250
HSEISNLAGF EVEAIINPTN ADIDLKDDLG NTLEKKGGKE FVEAVLELRK
260 270 280 290 300
KNGPLEVAGA AISAGHGLPA KFVIHCNSPV WGADKCEELL EKTVKNCLAL
310 320 330 340 350
ADDRKLKSIA FPSIGSGRNG FPKQTAAQLI LKAISSYFVS TMSSSIKTVY
360 370
FMLFDSESIG IYVQEMAKLD AN

Note: Major form.

Length:372
Mass (Da):39,735
Last modified:January 23, 2007 - v3
Checksum:i076CF76A34FACAA0
GO
Isoform 1 (identifier: Q9QZQ8-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     198-217: NLIHSEISNLAGFEVEAIIN → QVVQADIASIDSDAVVH
     221-229: ADIDLKDDL → TDFYTGGEV

Show »
Length:369
Mass (Da):39,290
Checksum:i33F123DE5C9C46EC
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei198 – 21720NLIHS…EAIIN → QVVQADIASIDSDAVVH in isoform 1. 2 PublicationsVSP_017596Add
BLAST
Alternative sequencei221 – 2299ADIDLKDDL → TDFYTGGEV in isoform 1. 2 PublicationsVSP_017597

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF171080 mRNA. Translation: AAD53745.1.
AF171081 mRNA. Translation: AAD53746.1.
AB071988 mRNA. Translation: BAB68541.1.
BC006955 mRNA. Translation: AAH06955.1.
CCDSiCCDS26557.1. [Q9QZQ8-1]
CCDS49278.1. [Q9QZQ8-2]
RefSeqiNP_001152985.1. NM_001159513.1.
NP_001152986.1. NM_001159514.1. [Q9QZQ8-2]
NP_001152987.1. NM_001159515.1.
NP_036145.1. NM_012015.2. [Q9QZQ8-1]
UniGeneiMm.283802.
Mm.478369.

Genome annotation databases

EnsembliENSMUST00000016081; ENSMUSP00000016081; ENSMUSG00000015937. [Q9QZQ8-1]
ENSMUST00000045788; ENSMUSP00000038221; ENSMUSG00000015937. [Q9QZQ8-2]
GeneIDi26914.
KEGGimmu:26914.
UCSCiuc007qsf.2. mouse. [Q9QZQ8-1]
uc007qsg.2. mouse. [Q9QZQ8-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF171080 mRNA. Translation: AAD53745.1.
AF171081 mRNA. Translation: AAD53746.1.
AB071988 mRNA. Translation: BAB68541.1.
BC006955 mRNA. Translation: AAH06955.1.
CCDSiCCDS26557.1. [Q9QZQ8-1]
CCDS49278.1. [Q9QZQ8-2]
RefSeqiNP_001152985.1. NM_001159513.1.
NP_001152986.1. NM_001159514.1. [Q9QZQ8-2]
NP_001152987.1. NM_001159515.1.
NP_036145.1. NM_012015.2. [Q9QZQ8-1]
UniGeneiMm.283802.
Mm.478369.

3D structure databases

ProteinModelPortaliQ9QZQ8.
SMRiQ9QZQ8. Positions 10-117, 181-369.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi205061. 1 interaction.
IntActiQ9QZQ8. 3 interactions.
MINTiMINT-4121159.

PTM databases

PhosphoSiteiQ9QZQ8.

Proteomic databases

MaxQBiQ9QZQ8.
PaxDbiQ9QZQ8.
PRIDEiQ9QZQ8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000016081; ENSMUSP00000016081; ENSMUSG00000015937. [Q9QZQ8-1]
ENSMUST00000045788; ENSMUSP00000038221; ENSMUSG00000015937. [Q9QZQ8-2]
GeneIDi26914.
KEGGimmu:26914.
UCSCiuc007qsf.2. mouse. [Q9QZQ8-1]
uc007qsg.2. mouse. [Q9QZQ8-2]

Organism-specific databases

CTDi9555.
MGIiMGI:1349392. H2afy.

Phylogenomic databases

eggNOGiCOG2110.
GeneTreeiENSGT00760000119217.
HOGENOMiHOG000234653.
HOVERGENiHBG009342.
InParanoidiQ9QZQ8.
KOiK11251.
OMAiQVVQADI.
OrthoDBiEOG71G9VP.
PhylomeDBiQ9QZQ8.
TreeFamiTF332276.

Enzyme and pathway databases

ReactomeiREACT_264471. NoRC negatively regulates rRNA expression.
REACT_27235. Meiotic Recombination.
REACT_287050. Meiotic synapsis.
REACT_326896. NoRC negatively regulates rRNA expression.
REACT_351456. DNA methylation.
REACT_75800. Meiotic Synapsis.

Miscellaneous databases

ChiTaRSiH2afy. mouse.
NextBioi304793.
PROiQ9QZQ8.
SOURCEiSearch...

Gene expression databases

BgeeiQ9QZQ8.
CleanExiMM_H2AFY.
ExpressionAtlasiQ9QZQ8. baseline and differential.
GenevestigatoriQ9QZQ8.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR021171. Core_histone_macro-H2A.
IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
IPR002589. Macro_dom.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF01661. Macro. 1 hit.
[Graphical view]
PIRSFiPIRSF037942. Core_histone_macro-H2A. 1 hit.
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00506. A1pp. 1 hit.
SM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS51154. MACRO. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Messenger RNAs encoding mouse histone macroH2A1 isoforms are expressed at similar levels in male and female cells and result from alternative splicing."
    Rasmussen T.P., Huang T., Mastrangelo M.-A., Loring J., Panning B., Jaenisch R.
    Nucleic Acids Res. 27:3685-3689(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), NUCLEOTIDE SEQUENCE [MRNA] OF 197-229 (ISOFORM 1), TISSUE SPECIFICITY.
    Strain: 129/SvEvTacfBr.
  2. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), INTERACTION WITH SPOP.
    Tissue: Brain.
  3. "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] (ISOFORM 1).
    Strain: FVB/N.
    Tissue: Mammary gland.
  4. "Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals."
    Costanzi C., Pehrson J.R.
    Nature 393:599-601(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  5. "MACROH2A2, a new member of the MACROH2A core histone family."
    Costanzi C., Pehrson J.R.
    J. Biol. Chem. 276:21776-21784(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY.
  6. "Dynamic relocation of epigenetic chromatin markers reveals an active role of constitutive heterochromatin in the transition from proliferation to quiescence."
    Grigoryev S.A., Nikitina T., Pehrson J.R., Singh P.B., Woodcock C.L.
    J. Cell Sci. 117:6153-6162(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  7. Cited for: INTERACTION WITH HDAC1 AND HDAC2, FUNCTION.
  8. "The phagosomal proteome in interferon-gamma-activated macrophages."
    Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
    Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-129, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-116 AND LYS-123, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.

Entry informationi

Entry nameiH2AY_MOUSE
AccessioniPrimary (citable) accession number: Q9QZQ8
Secondary accession number(s): Q91VZ2, Q9QZQ7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: January 23, 2007
Last modified: May 27, 2015
This is version 120 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.