MTREX Gene

Name Mtr4 exosome RNA helicase
Description 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, Mar 2025]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nMTR4 is a Ski2-like RNA helicase that acts as a central co‐factor for the nuclear exosome. It functions by bridging the exosome to distinct RNA‐binding adaptor proteins that target specific classes of nuclear RNAs for degradation. For example, MTR4 is part of the NEXT complex that targets early or improperly processed transcripts, and it is also linked via the PAXT connection to process longer, polyadenylated RNAs. In addition, MTR4 is required for efficient rRNA processing by cooperating with adaptor proteins such as MPP6 and C1D, and its depletion leads to the accumulation of unprocessed rRNA precursors and unstable long noncoding RNAs, which disrupt normal RNA homeostasis."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nMechanistically, MTR4’s function is intricately regulated by its interactions with various proteins that both facilitate and restrict its role in exosome recruitment. MTR4 competes with the mRNA export adaptor ALYREF for binding to ARS2, thereby determining whether a transcript is marked for export or degradation. Moreover, aberrant overexpression of MTR4—as observed in hepatocellular carcinoma—can drive metabolic reprogramming by ensuring appropriate alternative splicing of glycolytic genes. Structural studies have revealed that MTR4 recruits adaptors (such as ZCCHC8 and NVL via short linear AIM motifs in its arch domain) and is strategically positioned at the entrance of the RNA channel within the nuclear exosome. In contrast, regulatory proteins such as NRDE2 bind MTR4, locking it in a closed conformation and preventing its association with other recruitment factors, while studies involving TRAMP‐like components indicate that MTR4’s presence is not essential for assembling certain nucleolar RNA surveillance complexes."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "4", "end_ref": "9"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAdditional studies have broadened the functional landscape of MTR4 by identifying its integration into larger ribonucleoprotein machineries. Its association with factors such as WDR74 has been implicated in the remodeling of ribosomal assembly complexes, while reviews of its structural attributes underscore its versatility in RNA substrate recognition and processing. The zinc‐finger domain of ARS2 is critical for mediating interactions with MTR4 in the poly(A) tail exosome targeting pathway, pointing to coordinated regulation of RNA fate. In infection models, pathogen‐induced alterations result in the loss of MTR4 (and RRP6), leading to nuclear RNA accumulation that impacts host cell physiology. Finally, interactions with splicing regulators like SPF30 and pre‐rRNA processing factors such as PICT1 further link MTR4 to diverse aspects of RNA metabolism and ribosome biogenesis."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "10", "end_ref": "15"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Nicola Meola, Michal Domanski, Evdoxia Karadoulama, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.302604.117"}], "href": "https://doi.org/10.1101/gad.302604.117"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28733371"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28733371"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Jing Fan, Bin Kuai, Guifen Wu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "EMBO J (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.15252/embj.201696139"}], "href": "https://doi.org/10.15252/embj.201696139"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28801509"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28801509"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Lili Yu, Jinchul Kim, Lei Jiang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "MTR4 drives liver tumorigenesis by promoting cancer metabolic switch through alternative splicing."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41467-020-14437-3"}], "href": "https://doi.org/10.1038/s41467-020-14437-3"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "32024842"}], "href": "https://pubmed.ncbi.nlm.nih.gov/32024842"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Mahesh Lingaraju, Dennis Johnsen, Andreas Schlundt, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.322602.118"}], "href": "https://doi.org/10.1101/gad.322602.118"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30842217"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30842217"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Haruka Sudo, Aya Nozaki, Hideaki Uno, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Interaction properties of human TRAMP-like proteins and their role in pre-rRNA 5'ETS turnover."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "FEBS Lett (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/1873-3468.12314"}], "href": "https://doi.org/10.1002/1873-3468.12314"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27434818"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27434818"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Nobuhiro Hiraishi, Yo-ichi Ishida, Masami Nagahama "}, {"type": "b", "children": [{"type": "t", "text": "AAA-ATPase NVL2 acts on MTR4-exosome complex to dissociate the nucleolar protein WDR74."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochem Biophys Res Commun (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbrc.2015.09.160"}], "href": "https://doi.org/10.1016/j.bbrc.2015.09.160"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26456651"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26456651"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Keith J Olsen, Sean J Johnson "}, {"type": "b", "children": [{"type": "t", "text": "Mtr4 RNA helicase structures and interactions."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biol Chem (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1515/hsz-2020-0329"}], "href": "https://doi.org/10.1515/hsz-2020-0329"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33857361"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33857361"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Mireille Melko, Kinga Winczura, Jérôme Olivier Rouvière, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "MTR4 adaptor PICT1 functions in two distinct steps during pre-rRNA processing."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochem Biophys Res Commun (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbrc.2022.11.018"}], "href": "https://doi.org/10.1016/j.bbrc.2022.11.018"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36403484"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36403484"}]}]}]}
NCBI Gene ID 23517
API
Download Associations
Predicted Functions View MTREX's ARCHS4 Predicted Functions.
Co-expressed Genes View MTREX's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View MTREX's ARCHS4 Predicted Functions.

Functional Associations

MTREX has 2,567 functional associations with biological entities spanning 6 categories (chemical, functional term, phrase or reference, disease, phenotype or trait, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 37 datasets.

Click the + buttons to view associations for MTREX from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles tissue samples with high or low expression of MTREX gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
Carcinogenome Chemical Perturbation Carcinogenicity Signatures small molecule perturbations changing expression of MTREX gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
CCLE Cell Line Proteomics Cell lines associated with MTREX protein from the CCLE Cell Line Proteomics dataset.
CellMarker Gene-Cell Type Associations cell types associated with MTREX gene from the CellMarker Gene-Cell Type Associations dataset.
ChEA Transcription Factor Targets 2022 transcription factors binding the promoter of MTREX gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
CM4AI KOLF21J CRISPRi Gene Perturbation Atlas gene perturbations changing expression of MTREX gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores 2025 cellular components containing MTREX protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 cellular components co-occuring with MTREX protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 diseases co-occuring with MTREX gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
DisGeNET Gene-Disease Associations diseases associated with MTREX gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
GO Biological Process Annotations 2023 biological processes involving MTREX gene from the curated GO Biological Process Annotations 2023 dataset.
GO Biological Process Annotations 2025 biological processes involving MTREX gene from the curated GO Biological Process Annotations2025 dataset.
GO Cellular Component Annotations 2023 cellular components containing MTREX protein from the curated GO Cellular Component Annotations 2023 dataset.
GO Cellular Component Annotations 2025 cellular components containing MTREX protein from the curated GO Cellular Component Annotations 2025 dataset.
GO Molecular Function Annotations 2023 molecular functions performed by MTREX gene from the curated GO Molecular Function Annotations 2023 dataset.
GO Molecular Function Annotations 2025 molecular functions performed by MTREX gene from the curated GO Molecular Function Annotations 2025 dataset.
GTEx eQTL 2025 SNPs regulating expression of MTREX gene from the GTEx eQTL 2025 dataset.
GTEx Tissue Gene Expression Profiles 2023 tissues with high or low expression of MTREX gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
GTEx Tissue-Specific Aging Signatures tissue samples with high or low expression of MTREX gene relative to other tissue samples from the GTEx Tissue-Specific Aging Signatures dataset.
GWAS Catalog SNP-Phenotype Associations 2025 phenotypes associated with MTREX gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset.
JASPAR Predicted Human Transcription Factor Targets 2025 transcription factors regulating expression of MTREX gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset.
JASPAR Predicted Mouse Transcription Factor Targets 2025 transcription factors regulating expression of MTREX gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Mouse Transcription Factor Targets 2025 dataset.
KEGG Pathways 2026 pathways involving MTREX protein from the KEGG Pathways 2026 dataset.
LINCS L1000 CMAP Chemical Perturbation Consensus Signatures small molecule perturbations changing expression of MTREX gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset.
LINCS L1000 CMAP CRISPR Knockout Consensus Signatures gene perturbations changing expression of MTREX gene from the LINCS L1000 CMAP CRISPR Knockout Consensus Signatures dataset.
NIBR DRUG-seq U2OS MoA Box Gene Expression Profiles drug perturbations changing expression of MTREX gene from the NIBR DRUG-seq U2OS MoA Box dataset.
Reactome Pathways 2024 pathways involving MTREX protein from the Reactome Pathways 2024 dataset.
Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of MTREX gene from the Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures dataset.
Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of MTREX gene from the Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures dataset.
Rummagene Transcription Factor Associations 2026 transcription factors regulating expression of MTREX gene from the Rummagene Transcription Factor Associations 2026 dataset.
RummaGEO Drug Perturbation Signatures drug perturbations changing expression of MTREX gene from the RummaGEO Drug Perturbation Signatures dataset.
RummaGEO Gene Perturbation Signatures gene perturbations changing expression of MTREX gene from the RummaGEO Gene Perturbation Signatures dataset.
Sci-Plex Drug Perturbation Signatures drug perturbations changing expression of MTREX gene from the Sci-Plex Drug Perturbation Signatures dataset.
Tahoe Therapeutics Tahoe 100M Perturbation Atlas drug perturbations changing expression of MTREX gene from the Tahoe Therapeutics Tahoe 100M Perturbation Atlas dataset.
TISSUES Curated Tissue Protein Expression Evidence Scores 2025 tissues with high expression of MTREX protein from the TISSUES Curated Tissue Protein Expression Evidence Scores 2025 dataset.
TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 tissues with high expression of MTREX protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 dataset.
TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 tissues co-occuring with MTREX protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset.