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    DNMT1 DNA methyltransferase 1 [ Homo sapiens (human) ]

    Gene ID: 1786, updated on 10-Dec-2017
    Official Symbol
    DNMT1provided by HGNC
    Official Full Name
    DNA methyltransferase 1provided by HGNC
    Primary source
    HGNC:HGNC:2976
    See related
    Ensembl:ENSG00000130816 MIM:126375; Vega:OTTHUMG00000180397
    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
    Also known as
    AIM; DNMT; MCMT; CXXC9; HSN1E; ADCADN; m.HsaI
    Summary
    This gene encodes an enzyme that transfers methyl groups to cytosine nucleotides of genomic DNA. This protein is the major enzyme responsible for maintaining methylation patterns following DNA replication and shows a preference for hemi-methylated DNA. Methylation of DNA is an important component of mammalian epigenetic gene regulation. Aberrant methylation patterns are found in human tumors and associated with developmental abnormalities. Variation in this gene has been associated with cerebellar ataxia, deafness, and narcolepsy, and neuropathy, hereditary sensory, type IE. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
    Expression
    Broad expression in placenta (RPKM 28.0), lymph node (RPKM 23.6) and 24 other tissues See more
    Orthologs
    Location:
    19p13.2
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 19 NC_000019.10 (10133344..10195135, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10244021..10305783, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene PPAN-P2RY11 readthrough Neighboring gene small nucleolar RNA, C/D box 105B Neighboring gene peter pan homolog (Drosophila) Neighboring gene purinergic receptor P2Y11 Neighboring gene eukaryotic translation initiation factor 3 subunit G Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 10 pseudogene Neighboring gene sphingosine-1-phosphate receptor 2 Neighboring gene microRNA 4322

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Genome wide analysis of narcolepsy in China implicates novel immune loci and reveals changes in association prior to versus after the 2009 H1N1 influenza pandemic.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat upregulates DNMT1, DNMT3A, and DNMT3B both at the mRNA and protein levels in primary tumors PubMed

    Go to the HIV-1, Human Interaction Database

    • Cysteine and methionine metabolism, organism-specific biosystem (from KEGG)
      Cysteine and methionine metabolism, organism-specific biosystemCysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants, cysteine is converted f...
    • Cysteine and methionine metabolism, conserved biosystem (from KEGG)
      Cysteine and methionine metabolism, conserved biosystemCysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants, cysteine is converted f...
    • Cytosine methylation, organism-specific biosystem (from WikiPathways)
      Cytosine methylation, organism-specific biosystemDNA, namely cytosine, methylation is the key event in epigentics. The degree of methylation influences gene expression and methylation disorders are known to be major causes of some diseases like Ret...
    • DNA methylation, organism-specific biosystem (from REACTOME)
      DNA methylation, organism-specific biosystemMethylation of cytosine is catalyzed by a family of DNA methyltransferases (DNMTs): DNMT1, DNMT3A, and DNMT3B transfer methyl groups from S-adenosylmethionine to cytosine, producing 5-methylcytosine ...
    • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
      Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • Hematopoietic Stem Cell Gene Regulation by GABP alpha/beta Complex, organism-specific biosystem (from WikiPathways)
      Hematopoietic Stem Cell Gene Regulation by GABP alpha/beta Complex, organism-specific biosystemGABP alpha/beta complex mediates the maintenance of hematopoietic stem cells (HSCs) through control of proteins necessary for epigenetic modification and transcription regulation. The activation of k...
    • Metabolic pathways, organism-specific biosystem (from KEGG)
      Metabolic pathways, organism-specific biosystem
      Metabolic pathways
    • Methionine degradation, organism-specific biosystem (from KEGG)
      Methionine degradation, organism-specific biosystemPathway module; Nucleotide and amino acid metabolism; Cysteine and methionine metabolism
    • Methionine degradation, conserved biosystem (from KEGG)
      Methionine degradation, conserved biosystemPathway module; Nucleotide and amino acid metabolism; Cysteine and methionine metabolism
    • MicroRNAs in cancer, organism-specific biosystem (from KEGG)
      MicroRNAs in cancer, organism-specific biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
    • MicroRNAs in cancer, conserved biosystem (from KEGG)
      MicroRNAs in cancer, conserved biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
    • Negative epigenetic regulation of rRNA expression, organism-specific biosystem (from REACTOME)
      Negative epigenetic regulation of rRNA expression, organism-specific biosystemTranscription of rRNA genes is controlled by epigenetic activation and repression (reviewed in McStay and Grummt 2008, Goodfellow and Zomerdijk 2012, Grummt and Langst 2013). About half of the roughl...
    • NoRC negatively regulates rRNA expression, organism-specific biosystem (from REACTOME)
      NoRC negatively regulates rRNA expression, organism-specific biosystemOnly about half of the rRNA gene copies in a cell are expressed. The remaining copies are silenced by modifications to histones and DNA (reviewed in Santoro and Grummt 2001, Grummt 2007, Preuss and P...
    • One Carbon Metabolism, organism-specific biosystem (from WikiPathways)
      One Carbon Metabolism, organism-specific biosystemThis one-carbon metabolism pathway is centered around folate. Folate has two key carbon-carbon double bonds. Saturating one of them yields dihydrofolate (DHF) and adding an additional molecule of hyd...
    • PRC2 methylates histones and DNA, organism-specific biosystem (from REACTOME)
      PRC2 methylates histones and DNA, organism-specific biosystemPolycomb group proteins are responsible for the heritable repression of genes during development (Lee et al. 2006, Ku et al. 2008, reviewed in Simon and Kingston 2009, Margueron and Reinberg 2011, Di...
    • Regulation of retinoblastoma protein, organism-specific biosystem (from Pathway Interaction Database)
      Regulation of retinoblastoma protein, organism-specific biosystem
      Regulation of retinoblastoma protein
    • Retinoblastoma (RB) in Cancer, organism-specific biosystem (from WikiPathways)
      Retinoblastoma (RB) in Cancer, organism-specific biosystemDescribes the role of retinoblastoma (RB) gene in cancer.
    • Trans-sulfuration and one carbon metabolism, organism-specific biosystem (from WikiPathways)
      Trans-sulfuration and one carbon metabolism, organism-specific biosystem
      Trans-sulfuration and one carbon metabolism
    • Trans-sulfuration pathway, organism-specific biosystem (from WikiPathways)
      Trans-sulfuration pathway, organism-specific biosystemTrans-sulfuration pathway, the pathway of production of GSH from S-adenosylmethionine (SAMe). Evidences have been showed that this pathway was perturbed in liver toxicity studies.
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Potential readthrough

    Included gene: S1PR2

    Homology

    Clone Names

    • FLJ16293, MGC104992

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA (cytosine-5-)-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    DNA-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    DNA-methyltransferase activity TAS
    Traceable Author Statement
    more info
     
    RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    methyl-CpG binding IEA
    Inferred from Electronic Annotation
    more info
     
    promoter-specific chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    C-5 methylation of cytosine IEA
    Inferred from Electronic Annotation
    more info
     
    DNA methylation TAS
    Traceable Author Statement
    more info
    PubMed 
    DNA methylation involved in embryo development IEA
    Inferred from Electronic Annotation
    more info
     
    Ras protein signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular response to amino acid stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    covalent chromatin modification IEA
    Inferred from Electronic Annotation
    more info
     
    gene silencing IEA
    Inferred from Electronic Annotation
    more info
     
    maintenance of DNA methylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of gene expression, epigenetic TAS
    Traceable Author Statement
    more info
     
    negative regulation of histone H3-K9 methylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of histone H3-K4 methylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of methylation-dependent chromatin silencing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    pericentric heterochromatin IEA
    Inferred from Electronic Annotation
    more info
     
    replication fork IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    DNA (cytosine-5)-methyltransferase 1
    Names
    CXXC-type zinc finger protein 9
    DNA (cytosine-5-)-methyltransferase 1
    DNA MTase HsaI
    DNA methyltransferase HsaI
    NP_001124295.1
    NP_001305659.1
    NP_001305660.1
    NP_001370.1

    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.

    Genomic

    1. NG_028016.3 RefSeqGene

      Range
      41208..102941
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_362

    mRNA and Protein(s)

    1. NM_001130823.2NP_001124295.1  DNA (cytosine-5)-methyltransferase 1 isoform a

      See identical proteins and their annotated locations for NP_001124295.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as Dnmt1b in PMIDs 10449766 and 10753866) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      BC092517, BC126227, DA653750, HY245803, X63692
      Consensus CDS
      CCDS45958.1
      UniProtKB/Swiss-Prot
      P26358
      UniProtKB/TrEMBL
      I6L9H2
      Related
      ENSP00000352516.3, OTTHUMP00000264207, ENST00000359526.8, OTTHUMT00000451169
      Conserved Domains (6) summary
      COG0270
      Location:11541608
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd04711
      Location:9811117
      BAH_Dnmt1_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      cd04760
      Location:770893
      BAH_Dnmt1_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      pfam02008
      Location:661707
      zf-CXXC; CXXC zinc finger domain
      pfam06464
      Location:16105
      DMAP_binding; DMAP1-binding Domain
      pfam12047
      Location:415550
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
    2. NM_001318730.1NP_001305659.1  DNA (cytosine-5)-methyltransferase 1 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has a shorter 5' UTR, lacks an alternate in-frame exon in the 5' coding region, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AB209413, BC092517, BC126227, BX379258, DA653750, HY245803, X63692
      UniProtKB/Swiss-Prot
      P26358
      UniProtKB/TrEMBL
      I6L9H2, Q59FP7
      Conserved Domains (6) summary
      COG0270
      Location:11381595
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd04711
      Location:9651101
      BAH_Dnmt1_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      cd04760
      Location:754877
      BAH_Dnmt1_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      pfam02008
      Location:645691
      zf-CXXC; CXXC zinc finger domain
      pfam06464
      Location:16105
      DMAP_binding; DMAP1-binding Domain
      pfam12047
      Location:399534
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
    3. NM_001318731.1NP_001305660.1  DNA (cytosine-5)-methyltransferase 1 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has a shorter 5' UTR, uses an alternate splice site in the 5' region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (d) has a shorter N-terminus than isoform a.
      Source sequence(s)
      BC092517, BX379258, DA653750, HY245803, X63692
      UniProtKB/Swiss-Prot
      P26358
      UniProtKB/TrEMBL
      I6L9H2
      Related
      ENSP00000440457.2, ENST00000540357.5
      Conserved Domains (5) summary
      COG0270
      Location:10331487
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd04711
      Location:860996
      BAH_Dnmt1_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      cd04760
      Location:649772
      BAH_Dnmt1_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      pfam02008
      Location:540586
      zf-CXXC; CXXC zinc finger domain
      pfam12047
      Location:294429
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
    4. NM_001379.3NP_001370.1  DNA (cytosine-5)-methyltransferase 1 isoform b

      See identical proteins and their annotated locations for NP_001370.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as Dnmt1a in PMIDs 10449766 and 10753866) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting isoform (b) is shorter than isoform a.
      Source sequence(s)
      BC092517, BC126227, DA653750, HY245803, X63692
      Consensus CDS
      CCDS12228.1
      UniProtKB/Swiss-Prot
      P26358
      UniProtKB/TrEMBL
      I6L9H2
      Related
      ENSP00000345739.3, OTTHUMP00000264205, ENST00000340748.8, OTTHUMT00000451166
      Conserved Domains (6) summary
      COG0270
      Location:11381592
      Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]
      cd04711
      Location:9651101
      BAH_Dnmt1_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      cd04760
      Location:754877
      BAH_Dnmt1_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG ...
      pfam02008
      Location:645691
      zf-CXXC; CXXC zinc finger domain
      pfam06464
      Location:16105
      DMAP_binding; DMAP1-binding Domain
      pfam12047
      Location:399534
      DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p7 Primary Assembly

      Range
      10133344..10195135 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018930.2 Alternate CHM1_1.1

      Range
      10244305..10306077 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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