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

Gene ID: 116447, updated on 3-Apr-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
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Genomic context

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Location:
8q24.3
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (143309324..143359977, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (144456634..144507610, complement)
105.20220307 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. Functional characterization of two variants of mitochondrial topoisomerase TOP1MT that impact regulation of the mitochondrial genome. Al Khatib I, et al. J Biol Chem, 2022 Oct. PMID 36030054, Free PMC Article
  2. TOP1MT deficiency promotes GC invasion and migration via the enhancements of LDHA expression and aerobic glycolysis. Wang H, et al. Endocr Relat Cancer, 2017 Nov. PMID 28874393, Free PMC Article
  3. Effect of oxindolimine copper(II) and zinc(II) complexes on human topoisomerase I activity. Katkar P, et al. Metallomics, 2014 Jan. PMID 24172750
  4. Role of human topoisomerase IB on ionizing radiation induced damage. Jahan Z, et al. Biochem Biophys Res Commun, 2013 Mar 15. PMID 23422507
  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 (33) 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)

Genotypes

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 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_2023_10

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

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

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

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

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

  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

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

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

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

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

  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

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

  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

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

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

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

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

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

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

  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

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

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

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

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

  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

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

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

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