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    TOP1MT DNA topoisomerase I mitochondrial [ Homo sapiens (human) ]

    Gene ID: 116447, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TOP1MTprovided by HGNC
    Official Full Name
    DNA topoisomerase I mitochondrialprovided by HGNC
    Primary source
    HGNC:HGNC:29787
    See related
    Ensembl:ENSG00000184428 MIM:606387; AllianceGenome:HGNC:29787
    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
    Summary
    This gene encodes a mitochondrial DNA topoisomerase that plays a role in the modification of DNA topology. The encoded protein is a type IB topoisomerase and catalyzes the transient breaking and rejoining of DNA to relieve tension and DNA supercoiling generated in the mitochondrial genome during replication and transcription. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]
    Expression
    Ubiquitous expression in ovary (RPKM 11.4), bone marrow (RPKM 11.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TOP1MT in Genome Data Viewer
    Location:
    8q24.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (143309324..143359977, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (144456634..144507610, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (144391494..144442147, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144373076-144373651 Neighboring gene uncharacterized LOC124902037 Neighboring gene zinc finger protein 696 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144389476-144389976 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144389977-144390477 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144403237-144403900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144403901-144404564 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144404565-144405228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144405229-144405890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144414065-144414598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144416274-144416958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144421307-144422044 Neighboring gene RNA, U6 small nuclear 220, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144450004-144450559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144451300-144452207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144452208-144453114 Neighboring gene RHPN1 antisense RNA 1 (head to head) Neighboring gene rhophilin Rho GTPase binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144482673-144483320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144483321-144483968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144483969-144484616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144484617-144485263 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144487803-144488782 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19621 Neighboring gene MAFA antisense RNA 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
    • 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. Association of TOP1MT with immune infiltration and checkpoint in colorectal cance. Wang H, et al. Asian J Surg, 2024 Feb. PMID 37923603
    2. Human mitochondrial topoisomerase I. Zhang H, et al. Proc Natl Acad Sci U S A, 2001 Sep 11. PMID 11526219, Free PMC Article
    3. Mitochondrial topoisomerases and alternative splicing of the human TOP1mt gene. Zhang H, et al. Biochimie, 2007 Apr. PMID 17161897
    4. Adaptation of topoisomerase I paralogs to nuclear and mitochondrial DNA. Dalla Rosa I, et al. Nucleic Acids Res, 2009 Oct. PMID 19720733, Free PMC Article
    5. Coordinated regulation of mitochondrial topoisomerase IB with mitochondrial nuclear encoded genes and MYC. Zoppoli G, et al. Nucleic Acids Res, 2011 Aug. PMID 21531700, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association of TOP1MT with immune infiltration and checkpoint in colorectal cance.
      Title: Association of TOP1MT with immune infiltration and checkpoint in colorectal cance.
    2. Activation of the cGAS-STING innate immune response in cells with deficient mitochondrial topoisomerase TOP1MT.
      Title: Activation of the cGAS-STING innate immune response in cells with deficient mitochondrial topoisomerase TOP1MT.
    3. Functional characterization of two variants of mitochondrial topoisomerase TOP1MT that impact regulation of the mitochondrial genome.
      Title: Functional characterization of two variants of mitochondrial topoisomerase TOP1MT that impact regulation of the mitochondrial genome.
    4. Two type I topoisomerases maintain DNA topology in human mitochondria.
      Title: Two type I topoisomerases maintain DNA topology in human mitochondria.
    5. Study demonstrated that lack of TOP1MT results in delayed and decreased tumor growth due to impaired mitochondrial translation. The TOP1MT genomic signature profile, based on mouse model for Top1mt-KO liver cancers, is correlated with enhanced survival of hepatocellular carcinoma patients.
      Title: The mitochondrial type IB topoisomerase drives mitochondrial translation and carcinogenesis.
    6. This report was the first to focus on the role of TOP1MT in tumors. We identified a new mechanism underlying TOP1MT-deficient gastric cancer (GC) metastasis and showed that TOP1MT played an important role in cancer cells.
      Title: TOP1MT deficiency promotes GC invasion and migration via the enhancements of LDHA expression and aerobic glycolysis.
    7. Data indicate that the different coordination geometry achieved by the two transition metal ions has an important role in modulating their efficiency as topoisomerase I inhibitors.
      Title: Effect of oxindolimine copper(II) and zinc(II) complexes on human topoisomerase I activity.
    8. DNA topoisomerase I stimulates BLM helicase activity on a nucleolar-relevant RNA:DNA hybrid.
      Title: Collaborating functions of BLM and DNA topoisomerase I in regulating human rDNA transcription.
    9. Data reported in this paper indicate that hTop IB does not confer to the cells radio-resistance, but the kinetic analysis of both DNA repair rate as well as colonies growth, demonstrates that the cells containing hTop IB show a more efficient rescue from IR injury.
      Title: Role of human topoisomerase IB on ionizing radiation induced damage.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    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)

    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 DNA topoisomerase type I (single strand cut, ATP-independent) activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA replication IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA topological change IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in mitochondrial nucleoid IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrial nucleoid IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    DNA topoisomerase I, mitochondrial
    Names
    mitochondrial topoisomerase IB
    topoisomerase (DNA) I, mitochondrial
    NP_001245375.1
    NP_001245376.1
    NP_443195.1
    XP_005250838.1
    XP_047277286.1
    XP_047277287.1
    XP_047277288.1
    XP_047277289.1
    XP_047277290.1
    XP_047277291.1
    XP_047277292.1
    XP_047277294.1
    XP_047277295.1
    XP_047277296.1
    XP_047277297.1
    XP_047277298.1
    XP_047277299.1
    XP_047277300.1
    XP_047277301.1
    XP_047277302.1
    XP_054215701.1
    XP_054215702.1
    XP_054215703.1
    XP_054215704.1
    XP_054215705.1
    XP_054215706.1
    XP_054215707.1
    XP_054215708.1
    XP_054215709.1
    XP_054215710.1
    XP_054215711.1
    XP_054215712.1
    XP_054215713.1
    XP_054215714.1

    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_001258446.1 → NP_001245375.1  DNA topoisomerase I, mitochondrial isoform 2

      See identical proteins and their annotated locations for NP_001245375.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 2 and 3 encode the same isoform (2), which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AF349017, AK316380, AW248607, DC399840
      Consensus CDS
      CCDS59115.1
      UniProtKB/TrEMBL
      B4DYD2, B7Z9E8
      Related
      ENSP00000428369.1, ENST00000521193.5
      Conserved Domains (4) summary
      smart00435
      Location:98 → 474
      TOPEUc; DNA Topoisomerase I (eukaryota)
      pfam01028
      Location:171 → 373
      Topoisom_I; Eukaryotic DNA topoisomerase I, catalytic core
      pfam02919
      Location:1 → 167
      Topoisom_I_N; Eukaryotic DNA topoisomerase I, DNA binding fragment
      pfam14370
      Location:433 → 501
      Topo_C_assoc; C-terminal topoisomerase domain

    2. NM_001258447.1 → NP_001245376.1  DNA topoisomerase I, mitochondrial isoform 2

      See identical proteins and their annotated locations for NP_001245376.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 2 and 3 encode the same isoform (2), which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AF349017, AK302372, AW248607
      Consensus CDS
      CCDS59115.1
      UniProtKB/TrEMBL
      B4DYD2, B7Z9E8
      Related
      ENSP00000429169.1, ENST00000519148.5
      Conserved Domains (4) summary
      smart00435
      Location:98 → 474
      TOPEUc; DNA Topoisomerase I (eukaryota)
      pfam01028
      Location:171 → 373
      Topoisom_I; Eukaryotic DNA topoisomerase I, catalytic core
      pfam02919
      Location:1 → 167
      Topoisom_I_N; Eukaryotic DNA topoisomerase I, DNA binding fragment
      pfam14370
      Location:433 → 501
      Topo_C_assoc; C-terminal topoisomerase domain

    3. NM_052963.3 → NP_443195.1  DNA topoisomerase I, mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_443195.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AF349017, AW248607
      Consensus CDS
      CCDS6400.1
      UniProtKB/Swiss-Prot
      B7ZAR5, E7ES89, Q86ST4, Q86V82, Q969P6
      UniProtKB/TrEMBL
      E5KMK5, E5KMK6, E5KMK7
      Related
      ENSP00000328835.3, ENST00000329245.9
      Conserved Domains (4) summary
      smart00435
      Location:196 → 572
      TOPEUc; DNA Topoisomerase I (eukaryota)
      pfam01028
      Location:269 → 471
      Topoisom_I; Eukaryotic DNA topoisomerase I, catalytic core
      pfam02919
      Location:51 → 265
      Topoisom_I_N; Eukaryotic DNA topoisomerase I, DNA binding fragment
      pfam14370
      Location:531 → 599
      Topo_C_assoc; C-terminal topoisomerase 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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      143309324..143359977 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047421333.1 → XP_047277289.1  DNA topoisomerase I, mitochondrial isoform X5

      UniProtKB/TrEMBL
      E5KMK5, E5KMK6

    2. XM_047421346.1 → XP_047277302.1  DNA topoisomerase I, mitochondrial isoform X9

      UniProtKB/TrEMBL
      E5KMK5, E5KMK6

    3. XM_047421334.1 → XP_047277290.1  DNA topoisomerase I, mitochondrial isoform X6

      UniProtKB/TrEMBL
      E5KMK5, E5KMK6

    4. XM_047421336.1 → XP_047277292.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    5. XM_047421339.1 → XP_047277295.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    6. XM_047421330.1 → XP_047277286.1  DNA topoisomerase I, mitochondrial isoform X1

    7. XM_047421342.1 → XP_047277298.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    8. XM_047421332.1 → XP_047277288.1  DNA topoisomerase I, mitochondrial isoform X4

      UniProtKB/TrEMBL
      E5KMK5, E5KMK6

    9. XM_047421338.1 → XP_047277294.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    10. XM_047421344.1 → XP_047277300.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    11. XM_047421340.1 → XP_047277296.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    12. XM_005250781.5 → XP_005250838.1  DNA topoisomerase I, mitochondrial isoform X3

      UniProtKB/TrEMBL
      E5KMK5, E5KMK6
      Conserved Domains (4) summary
      smart00435
      Location:196 → 569
      TOPEUc; DNA Topoisomerase I (eukaryota)
      pfam01028
      Location:269 → 471
      Topoisom_I; Eukaryotic DNA topoisomerase I, catalytic core
      pfam02919
      Location:51 → 265
      Topoisom_I_N; Eukaryotic DNA topoisomerase I, DNA binding fragment
      pfam14370
      Location:531 → 569
      Topo_C_assoc; C-terminal topoisomerase domain

    13. XM_047421335.1 → XP_047277291.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    14. XM_047421341.1 → XP_047277297.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    15. XM_047421331.1 → XP_047277287.1  DNA topoisomerase I, mitochondrial isoform X2

    16. XM_047421343.1 → XP_047277299.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    17. XM_047421345.1 → XP_047277301.1  DNA topoisomerase I, mitochondrial isoform X8

      UniProtKB/TrEMBL
      E5KMK6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      144456634..144507610 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359730.1 → XP_054215705.1  DNA topoisomerase I, mitochondrial isoform X5

      UniProtKB/TrEMBL
      E5KMK6

    2. XM_054359739.1 → XP_054215714.1  DNA topoisomerase I, mitochondrial isoform X9

      UniProtKB/TrEMBL
      E5KMK6

    3. XM_054359731.1 → XP_054215706.1  DNA topoisomerase I, mitochondrial isoform X6

      UniProtKB/TrEMBL
      E5KMK6

    4. XM_054359733.1 → XP_054215708.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    5. XM_054359734.1 → XP_054215709.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    6. XM_054359726.1 → XP_054215701.1  DNA topoisomerase I, mitochondrial isoform X1

    7. XM_054359736.1 → XP_054215711.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    8. XM_054359729.1 → XP_054215704.1  DNA topoisomerase I, mitochondrial isoform X4

      UniProtKB/TrEMBL
      E5KMK6

    9. XM_054359728.1 → XP_054215703.1  DNA topoisomerase I, mitochondrial isoform X3

      UniProtKB/TrEMBL
      E5KMK6

    10. XM_054359732.1 → XP_054215707.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    11. XM_054359735.1 → XP_054215710.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    12. XM_054359727.1 → XP_054215702.1  DNA topoisomerase I, mitochondrial isoform X2

    13. XM_054359737.1 → XP_054215712.1  DNA topoisomerase I, mitochondrial isoform X7

      UniProtKB/TrEMBL
      B4E061

    14. XM_054359738.1 → XP_054215713.1  DNA topoisomerase I, mitochondrial isoform X8

      UniProtKB/TrEMBL
      E5KMK6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969P6.1 GenPept UniProtKB/Swiss-Prot:Q969P6

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