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UBN1 ubinuclein 1 [ Homo sapiens (human) ]

Gene ID: 29855, updated on 11-Apr-2024

Summary

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Official Symbol
UBN1provided by HGNC
Official Full Name
ubinuclein 1provided by HGNC
Primary source
HGNC:HGNC:12506
See related
Ensembl:ENSG00000118900 MIM:609771; AllianceGenome:HGNC:12506
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
VT; VT4
Summary
Cellular senescence is a hallmark of tumor suppression and tissue aging. Senescent cells contain domains of heterochromatin, called senescence-associated heterochromatin foci (SAHF), that repress proliferation-promoting genes. The protein encoded by this gene binds to proliferation-promoting genes and is required for SAHF formation, enhancing methylation of histone H3. [provided by RefSeq, Oct 2016]
Expression
Broad expression in testis (RPKM 22.1), bone marrow (RPKM 13.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16p13.3
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (4847481..4882401)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (4876971..4911890)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (4897482..4932402)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4852142-4852642 Neighboring gene Sharpr-MPRA regulatory region 4562 Neighboring gene rogdi atypical leucine zipper Neighboring gene glyoxylate reductase 1 homolog Neighboring gene uncharacterized LOC124903638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10346 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:4897448-4898290 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:4901871-4903070 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:4908973-4910172 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:4920799-4920984 Neighboring gene MPRA-validated peak2474 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4935135-4935635 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:4945259-4946104 Neighboring gene uncharacterized LOC124903637 Neighboring gene periplakin Neighboring gene uncharacterized LOC105371064 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:4968443-4968998

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity. Ricketts MD, et al. J Biol Chem, 2019 Jun 7. PMID 31040182, Free PMC Article
  2. A Molecular Prospective for HIRA Complex Assembly and H3.3-Specific Histone Chaperone Function. Ricketts MD, et al. J Mol Biol, 2017 Jun 30. PMID 27871933, Free PMC Article
  3. Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex. Ricketts MD, et al. Nat Commun, 2015 Jul 10. PMID 26159857, Free PMC Article
  4. The nuclear and adherent junction complex component protein ubinuclein negatively regulates the productive cycle of Epstein-Barr virus in epithelial cells. Gruffat H, et al. J Virol, 2011 Jan. PMID 21084479, Free PMC Article
  5. Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit. Ray-Gallet D, et al. Nat Commun, 2018 Aug 6. PMID 30082790, Free PMC Article

See all (51) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells.
    Title: Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells.
  2. UBN1 may be capable of binding two H3.3/H4 molecules to facilitate (H3.3/H4)2 tetramer formation in a pathway to nucleosome deposition that may also involve UBN1-mediated DNA binding by the HIRA complex.
    Title: The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity.
  3. analysis of the trimeric HIRA, UBN1 and CABIN1 H3.3 histone chaperone complex
    Title: Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit.
  4. study points to UBN1 as the determinant of H3.3-specific binding and deposition by the HIRA histone chaperone complex.
    Title: Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex.
  5. NHRD domain of UBN1 as being an essential region for HIRA interaction and chromatin organization by the HUCA complex
    Title: Identification of an ubinuclein 1 region required for stability and function of the human HIRA/UBN1/CABIN1/ASF1a histone H3.3 chaperone complex.
  6. a 184-amino acid region (from amino acids 39 to 223) at the N-terminal region of Ubn-1 was responsible for the interaction with the PDZ2 domain of ZO-1
    Title: Identification of new interacting partners of the shuttling protein ubinuclein (Ubn-1).
  7. Data show that, like HIRA, UBN1, and ASF1a, CABIN1 is involved in heterochromatinization of the genome of senescent human cells.
    Title: Human CABIN1 is a functional member of the human HIRA/UBN1/ASF1a histone H3.3 chaperone complex.
  8. By a chromatin immunoprecipitation (ChIP) assay, the authors show that Ubn-1 blocks EB1-human herpesvirus 4 DNA interaction.
    Title: The nuclear and adherent junction complex component protein ubinuclein negatively regulates the productive cycle of Epstein-Barr virus in epithelial cells.
  9. Analyses have revealed that in most cells ubinuclein occurred in the nucleoplasm, but in cells forming tight junctions it is recruited to the plaque structure of the zonula occludens.
    Title: Characterization of the ubinuclein protein as a new member of the nuclear and adhesion complex components (NACos).
  10. Hpc2-related domain of UBN1, UBN2, and Hpc2p is an evolutionarily conserved HIRA/Hir-binding domain, which directly interacts with the N-terminal WD repeats of HIRA/Hir.
    Title: Human UBN1 is an ortholog of yeast Hpc2p and has an essential role in the HIRA/ASF1a chromatin-remodeling pathway in senescent cells.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nucleosome assembly IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in PML body IEA
Inferred from Electronic Annotation
more info
  
located_in bicellular tight junction ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in centriolar satellite IDA
Inferred from Direct Assay
more info
  
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ubinuclein-1
Names
HIRA-binding protein
ubiquitously expressed nuclear protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_051820.2 RefSeqGene

    Range
    5002..39922
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001079514.3 → NP_001072982.1  ubinuclein-1 isoform a

    See identical proteins and their annotated locations for NP_001072982.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longest transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC020663, AC027687
    Consensus CDS
    CCDS10525.1
    UniProtKB/Swiss-Prot
    B7Z6D3, D3DUE8, Q13079, Q9NPG3, Q9P1P7
    Related
    ENSP00000262376.5, ENST00000262376.11
    Conserved Domains (2) summary
    pfam08729
    Location:119 → 168
    HUN; HPC2 and ubinuclein domain
    pfam14075
    Location:360 → 573
    UBN_AB; Ubinuclein conserved middle domain

  2. NM_001288656.1 → NP_001275585.1  ubinuclein-1 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks an in-frame exon in the 3' coding region, compared to variant 2. The encoded isoform (b) is shorter, compared to isoform a.
    Source sequence(s)
    AF108460, AK300131, AU120544, BC013750, BG822152, BQ186272, CB242197, CV574190
    Consensus CDS
    CCDS73822.1
    UniProtKB/Swiss-Prot
    Q9NPG3
    Related
    ENSP00000468740.1, ENST00000590769.5
    Conserved Domains (2) summary
    pfam08729
    Location:119 → 168
    HUN; HPC2 and ubinuclein domain
    pfam14075
    Location:360 → 573
    UBN_AB; Ubinuclein conserved middle domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    4847481..4882401
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522465.3 → XP_011520767.1  ubinuclein-1 isoform X5

    Conserved Domains (2) summary
    pfam08729
    Location:119 → 168
    HUN; HPC2 and ubinuclein domain
    pfam14075
    Location:360 → 573
    UBN_AB; Ubinuclein conserved middle domain

  2. XM_017023190.3 → XP_016878679.1  ubinuclein-1 isoform X4

  3. XM_047434040.1 → XP_047289996.1  ubinuclein-1 isoform X6

  4. XM_005255277.5 → XP_005255334.1  ubinuclein-1 isoform X1

    See identical proteins and their annotated locations for XP_005255334.1

    Conserved Domains (2) summary
    pfam08729
    Location:119 → 168
    HUN; HPC2 and ubinuclein domain
    pfam14075
    Location:360 → 573
    UBN_AB; Ubinuclein conserved middle domain

  5. XM_005255279.5 → XP_005255336.1  ubinuclein-1 isoform X3

    Conserved Domains (2) summary
    pfam08729
    Location:119 → 168
    HUN; HPC2 and ubinuclein domain
    pfam14075
    Location:360 → 525
    UBN_AB; Ubinuclein conserved middle domain

  6. XM_017023192.3 → XP_016878681.1  ubinuclein-1 isoform X9

  7. XM_011522467.3 → XP_011520769.1  ubinuclein-1 isoform X10

    Conserved Domains (2) summary
    pfam08729
    Location:119 → 168
    HUN; HPC2 and ubinuclein domain
    pfam14075
    Location:360 → 569
    UBN_AB; Ubinuclein conserved middle domain

  8. XM_047434037.1 → XP_047289993.1  ubinuclein-1 isoform X2

    UniProtKB/Swiss-Prot
    B7Z6D3, D3DUE8, Q13079, Q9NPG3, Q9P1P7
    Related
    ENSP00000379894.3, ENST00000396658.8

  9. XM_047434039.1 → XP_047289995.1  ubinuclein-1 isoform X4

  10. XM_005255278.4 → XP_005255335.1  ubinuclein-1 isoform X1

    See identical proteins and their annotated locations for XP_005255335.1

    Conserved Domains (2) summary
    pfam08729
    Location:119 → 168
    HUN; HPC2 and ubinuclein domain
    pfam14075
    Location:360 → 573
    UBN_AB; Ubinuclein conserved middle domain

  11. XM_047434038.1 → XP_047289994.1  ubinuclein-1 isoform X3

  12. XM_047434041.1 → XP_047289997.1  ubinuclein-1 isoform X7

  13. XM_047434042.1 → XP_047289998.1  ubinuclein-1 isoform X8

RNA

  1. XR_007064874.1 RNA Sequence

  2. XR_007064875.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    4876971..4911890
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054380192.1 → XP_054236167.1  ubinuclein-1 isoform X5

  2. XM_054380190.1 → XP_054236165.1  ubinuclein-1 isoform X4

  3. XM_054380193.1 → XP_054236168.1  ubinuclein-1 isoform X6

  4. XM_054380195.1 → XP_054236170.1  ubinuclein-1 isoform X9

  5. XM_054380196.1 → XP_054236171.1  ubinuclein-1 isoform X10

  6. XM_054380189.1 → XP_054236164.1  ubinuclein-1 isoform X2

    UniProtKB/Swiss-Prot
    B7Z6D3, D3DUE8, Q13079, Q9NPG3, Q9P1P7

  7. XM_054380191.1 → XP_054236166.1  ubinuclein-1 isoform X4

  8. XM_054380194.1 → XP_054236169.1  ubinuclein-1 isoform X8

RNA

  1. XR_008489082.1 RNA Sequence

  2. XR_008489083.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_016936.3: Suppressed sequence

    Description
    NM_016936.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NPG3.2 GenPept UniProtKB/Swiss-Prot:Q9NPG3

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