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    MTREX Mtr4 exosome RNA helicase [ Homo sapiens (human) ]

    Gene ID: 23517, updated on 3-Nov-2024

    Summary

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    Official Symbol
    MTREXprovided by HGNC
    Official Full Name
    Mtr4 exosome RNA helicaseprovided by HGNC
    Primary source
    HGNC:HGNC:18734
    See related
    Ensembl:ENSG00000039123 MIM:618122; AllianceGenome:HGNC:18734
    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
    Dob1; Mtr4; SKIV2L2; fSAP118; KIAA0052
    Summary
    Enables ATP binding activity and RNA helicase activity. Involved in DNA damage response; RNA catabolic process; and maturation of 5.8S rRNA. Located in nuclear exosome (RNase complex) and nucleoplasm. Part of TRAMP complex and catalytic step 2 spliceosome. Biomarker of amyotrophic lateral sclerosis. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in prostate (RPKM 29.9), gall bladder (RPKM 23.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MTREX in Genome Data Viewer
    Location:
    5q11.2
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (55307989..55425579)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (56135296..56252888)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (54603817..54721407)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:54527615-54528254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:54528255-54528894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16013 Neighboring gene Sharpr-MPRA regulatory region 6084 Neighboring gene CCNO divergent transcript Neighboring gene cyclin O Neighboring gene DExH-box helicase 29 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22554 Neighboring gene uncharacterized LOC124900979 Neighboring gene protein serine kinase H1 pseudogene Neighboring gene uncharacterized LOC107986415 Neighboring gene uncharacterized LOC124900977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16015 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:54733965-54734792 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:54737283-54737821 Neighboring gene phospholipid phosphatase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:54797624-54798166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:54798167-54798709 Neighboring gene microRNA 5687 Neighboring gene ring finger protein 138 pseudogene 1

    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 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. MTR4 drives liver tumorigenesis by promoting cancer metabolic switch through alternative splicing. Yu L, et al. Nat Commun, 2020 Feb 5. PMID 32024842, Free PMC Article
    2. Mtr4 RNA helicase structures and interactions. Olsen KJ, et al. Biol Chem, 2021 Apr 27. PMID 33857361, Free PMC Article
    3. RNA helicase MTR4 drives tumorigenesis of nasopharyngeal carcinoma by regulating the expression of key cell cycle genes. Yu L, et al. Protein Cell, 2023 Mar 16. PMID 36929008, Free PMC Article
    4. MTR4 adaptor PICT1 functions in two distinct steps during pre-rRNA processing. Miyao S, et al. Biochem Biophys Res Commun, 2022 Dec 31. PMID 36403484
    5. NRDE-2, the human homolog of fission yeast Nrl1, prevents DNA damage accumulation in human cells. Richard P, et al. RNA Biol, 2018. PMID 29902117, Free PMC Article

    See all (191) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RNA helicase MTR4 drives tumorigenesis of nasopharyngeal carcinoma by regulating the expression of key cell cycle genes.
      Title: RNA helicase MTR4 drives tumorigenesis of nasopharyngeal carcinoma by regulating the expression of key cell cycle genes.
    2. MTR4 adaptor PICT1 functions in two distinct steps during pre-rRNA processing.
      Title: MTR4 adaptor PICT1 functions in two distinct steps during pre-rRNA processing.
    3. Mtr4 RNA helicase structures and interactions.
      Title: Mtr4 RNA helicase structures and interactions.
    4. Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2.
      Title: Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2.
    5. Exploration of Salmonella effector mutant strains on MTR4 and RRP6 degradation.
      Title: Exploration of Salmonella effector mutant strains on MTR4 and RRP6 degradation.
    6. Mapping domains of ARS2 critical for its RNA decay capacity.
      Title: Mapping domains of ARS2 critical for its RNA decay capacity.
    7. MTR4 is required for the tumorigenesis of the hepatocellular carcinoma cells.MTR4 is a mediator of the functions of c-Myc in cancer metabolism.MTR4 drives cancer metabolism by ensuring correct alternative splicing of pre-mRNAs of critical glycolytic genes such as GLUT1 and PKM2.
      Title: MTR4 drives liver tumorigenesis by promoting cancer metabolic switch through alternative splicing.
    8. Data show that the nuclear exosome adaptors nuclear valosin-containing protein-like (NVL) and zinc finger, CCHC domain containing 8 protein (ZCCHC8) bind the Mtr4 exosome RNA helicase (MTR4) KOW domain on a surface.
      Title: The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs.
    9. NRDE2 interacts with MTR4's key residues, locks MTR4 in a closed conformation, and inhibits MTR4 interaction with the exosome as well as proteins important for MTR4 recruitment
      Title: NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction.
    10. The cryo-EM structure of the holo-complex shows how obligate nuclear cofactors position the hMTR4 helicase at the entrance of the core complex, suggesting a striking structural conservation from lower to higher eukaryotes.
      Title: Distinct and evolutionary conserved structural features of the human nuclear exosome complex.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, superkiller viralicidic activity 2-like 2 (SKIV2L2), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • MGC142069

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA helicase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in RNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in RNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in maturation of 5.8S rRNA IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in maturation of 5.8S rRNA IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in rRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in snRNA catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of TRAMP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of TRAMP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of exosome (RNase complex) IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of nuclear exosome (RNase complex) IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    exosome RNA helicase MTR4
    Names
    ATP-dependent RNA helicase DOB1
    ATP-dependent RNA helicase SKIV2L2
    ATP-dependent helicase SKIV2L2
    Ski2 like RNA helicase 2
    TRAMP-like complex helicase
    functional spliceosome-associated protein 118
    superkiller viralicidic activity 2-like 2
    NP_056175.3

    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_015360.5 → NP_056175.3  exosome RNA helicase MTR4

      See identical proteins and their annotated locations for NP_056175.3

      Status: VALIDATED

      Source sequence(s)
      BC065258, BX640789
      Consensus CDS
      CCDS3967.1
      UniProtKB/Swiss-Prot
      P42285, Q2M386, Q6MZZ8, Q6P170, Q8N5R0, Q8TAG2
      UniProtKB/TrEMBL
      A8K6I4
      Related
      ENSP00000230640.5, ENST00000230640.10
      Conserved Domains (5) summary
      COG4581
      Location:68 → 1042
      Dob10; Superfamily II RNA helicase [Replication, recombination and repair]
      cd00079
      Location:374 → 538
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00270
      Location:144 → 287
      DEAD; DEAD/DEAH box helicase
      pfam08148
      Location:868 → 1035
      DSHCT; DSHCT (NUC185) domain
      pfam13234
      Location:584 → 840
      rRNA_proc-arch; rRNA-processing arch domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      55307989..55425579
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      56135296..56252888
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P42285.3 GenPept UniProtKB/Swiss-Prot:P42285

    Gene LinkOut

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