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YOD1 YOD1 deubiquitinase [ Homo sapiens (human) ]

Gene ID: 55432, updated on 5-Mar-2024

Summary

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Official Symbol
YOD1provided by HGNC
Official Full Name
YOD1 deubiquitinaseprovided by HGNC
Primary source
HGNC:HGNC:25035
See related
Ensembl:ENSG00000180667 MIM:612023; AllianceGenome:HGNC:25035
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DUBA8; OTUD2; PRO0907
Summary
Protein ubiquitination controls many intracellular processes, including cell cycle progression, transcriptional activation, and signal transduction. This dynamic process, involving ubiquitin conjugating enzymes and deubiquitinating enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are cysteine proteases that specifically cleave ubiquitin from ubiquitin-conjugated protein substrates. The protein encoded by this gene belongs to a DUB subfamily characterized by an ovarian tumor (OTU) domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
Expression
Broad expression in bone marrow (RPKM 24.5), esophagus (RPKM 15.7) and 23 other tissues See more
Orthologs
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Genomic context

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See YOD1 in Genome Data Viewer
Location:
1q32.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (207043849..207053116, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (206309040..206318351, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (207217194..207226461, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:207192892-207194091 Neighboring gene chromosome 1 open reading frame 116 Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 4428 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:207224117-207224687 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:207225911-207226550 Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:207240869-207241100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2439 Neighboring gene complement component 4 binding protein beta Neighboring gene uncharacterized LOC107985251 Neighboring gene complement component 4 binding protein alpha

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. Deubiquitinase YOD1: the potent activator of YAP in hepatomegaly and liver cancer. Kim Y, et al. BMB Rep, 2017 Jun. PMID 28502290, Free PMC Article
  2. Deubiquitinating enzyme YOD1 deubiquitinates and destabilizes α-synuclein. Park SS, et al. Biochem Biophys Res Commun, 2023 Feb 19. PMID 36682332
  3. Blockade of deubiquitinase YOD1 degrades oncogenic PML/RARα and eradicates acute promyelocytic leukemia cells. Shao X, et al. Acta Pharm Sin B, 2022 Apr. PMID 35847510, Free PMC Article
  4. miR-190a-3p Promotes Proliferation and Migration in Glioma Cells via YOD1. Zhou L, et al. Comput Math Methods Med, 2021. PMID 34527075, Free PMC Article
  5. Targeting YOD1 by RNA Interference Inhibits Proliferation and Migration of Human Oral Keratinocytes through Transforming Growth Factor-β3 Signaling Pathway. Zhou XL, et al. Biomed Res Int, 2018. PMID 30345304, Free PMC Article

See all (46) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Deubiquitylase YOD1 regulates CDK1 stability and drives triple-negative breast cancer tumorigenesis.
    Title: Deubiquitylase YOD1 regulates CDK1 stability and drives triple-negative breast cancer tumorigenesis.
  2. YY1-induced LncRNA-TUG1 elevates YOD1 to promote cell proliferation and inhibit bortezomib sensitivity in multiple myeloma.
    Title: YY1-induced LncRNA-TUG1 elevates YOD1 to promote cell proliferation and inhibit bortezomib sensitivity in multiple myeloma.
  3. Deubiquitinating enzyme YOD1 deubiquitinates and destabilizes alpha-synuclein.
    Title: Deubiquitinating enzyme YOD1 deubiquitinates and destabilizes α-synuclein.
  4. findings thus provided novel insights into the regulatory cascade of the cellular antiviral response through YOD1-mediated K63-linked deubiquitination and aggregation of MAVS.
    Title: The Otubain YOD1 Suppresses Aggregation and Activation of the Signaling Adaptor MAVS through Lys63-Linked Deubiquitination.
  5. YOD1 RNAi may inhibit cell proliferation and migration associated with the pathogenesis of NSCL/P through TGF-beta3 signaling. The study indicates a novel role of YOD1 in regulating TGF-beta3 signaling to affect cell proliferation and migration resulting in cleft lip with or without cleft palate.
    Title: Targeting YOD1 by RNA Interference Inhibits Proliferation and Migration of Human Oral Keratinocytes through Transforming Growth Factor-β3 Signaling Pathway.
  6. This study showed that YOD1 overexpression enhances cell migration by promoting TGF-beta3 signaling which may play an important role in lip and palate formation.
    Title: Overexpression of YOD1 Promotes the Migration of Human Oral Keratinocytes by Enhancing TGF-β3 Signaling.
  7. Mechanistically, YOD1 deubiquitinates ITCH, an E3 ligase of LATS, and enhances the stability of ITCH, which leads to reduced levels of LATS and a subsequent increase in the YAP/TAZ level.
    Title: Deubiquitinase YOD1 potentiates YAP/TAZ activities through enhancing ITCH stability.
  8. Data suggest that YOD1 is a novel regulator of the Hippo pathway, and thereby a potential therapeutic target for liver cancer.
    Title: Deubiquitinase YOD1: the potent activator of YAP in hepatomegaly and liver cancer.
  9. These data define that YOD1 antagonizes TRAF6/p62-dependent IL-1 signaling to NF-kappaB.
    Title: YOD1/TRAF6 association balances p62-dependent IL-1 signaling to NF-κB.
  10. Upon damage, p97 translocates to lysosomes and there cooperates with a distinct set of cofactors including UBXD1, PLAA, and the deubiquitinating enzyme YOD1, which we term ELDR components for Endo-Lysosomal Damage Response.
    Title: VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy.
Submit: New GeneRIF Correction See all GeneRIFs (13)

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

Clone Names

  • DKFZp451J1719

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables K48-linked deubiquitinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables K63-linked deubiquitinase activity TAS
Traceable Author Statement
more info
 PubMed 
enables cysteine-type deubiquitinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cysteine-type deubiquitinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables deubiquitinase activity TAS
Traceable Author Statement
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in ERAD pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ERAD pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum unfolded protein response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endoplasmic reticulum unfolded protein response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in macroautophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of retrograde protein transport, ER to cytosol IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein K11-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K11-linked deubiquitination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein K27-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K29-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K33-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K48-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K48-linked deubiquitination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein K63-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K63-linked deubiquitination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
ubiquitin thioesterase OTU1
Names
DUBA-8
HIN-7
HIV-1-induced protease 7
OTU domain containing 2
OTU domain-containing protein 2
YOD1 OTU deubiquinating enzyme 1 homolog ( yeast)
hsHIN7
NP_001263249.1
NP_061036.3
XP_047280403.1
XP_054193502.1

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.

mRNA and Protein(s)

  1. NM_001276320.2 → NP_001263249.1  ubiquitin thioesterase OTU1 isoform 2

    See identical proteins and their annotated locations for NP_001263249.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains alternate exons in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AL445493
    Consensus CDS
    CCDS60402.1
    UniProtKB/Swiss-Prot
    Q5VVQ6
    Related
    ENSP00000356051.1, ENST00000367084.1
    Conserved Domains (1) summary
    COG5539
    Location:47 → 303
    COG5539; Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]

  2. NM_018566.4 → NP_061036.3  ubiquitin thioesterase OTU1 isoform 1

    See identical proteins and their annotated locations for NP_061036.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL445493
    Consensus CDS
    CCDS31002.1
    UniProtKB/Swiss-Prot
    B2RNX3, Q5VVQ5, Q5VVQ6, Q6ZRS6, Q86T63, Q9P1L8
    Related
    ENSP00000326813.4, ENST00000315927.9
    Conserved Domains (1) summary
    COG5539
    Location:91 → 347
    COG5539; Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    207043849..207053116 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047424447.1 → XP_047280403.1  ubiquitin thioesterase OTU1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    206309040..206318351 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337527.1 → XP_054193502.1  ubiquitin thioesterase OTU1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VVQ6.1 GenPept UniProtKB/Swiss-Prot:Q5VVQ6

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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