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DNMT1 DNA (cytosine-5-)-methyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 1786, updated on 19-Jul-2016
Official Symbol
DNMT1provided by HGNC
Official Full Name
DNA (cytosine-5-)-methyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:2976
See related
Ensembl:ENSG00000130816 HPRD:00532; 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]
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...
  • 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...
  • 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...
  • RB in Cancer, organism-specific biosystem (from WikiPathways)
    RB in Cancer, organism-specific biosystem
    RB in Cancer
  • Regulation of retinoblastoma protein, organism-specific biosystem (from Pathway Interaction Database)
    Regulation of retinoblastoma protein, organism-specific biosystem
    Regulation of retinoblastoma protein
  • 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 (cytosine-5-)-methyltransferase activity, acting on CpG substrates IEA
Inferred from Electronic Annotation
more info
 
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
 
double-stranded DNA binding IEA
Inferred from Electronic Annotation
more info
 
estrogen receptor binding IEA
Inferred from Electronic Annotation
more info
 
histone deacetylase 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 
protein domain specific binding IEA
Inferred from Electronic Annotation
more info
 
unmethylated CpG binding IEA
Inferred from Electronic Annotation
more info
 
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 hypermethylation IEA
Inferred from Electronic Annotation
more info
 
DNA methylation TAS
Traceable Author Statement
more info
PubMed 
DNA methylation on cytosine within a CG sequence IEA
Inferred from Electronic Annotation
more info
 
Ras protein signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
S-adenosylhomocysteine metabolic process IEA
Inferred from Electronic Annotation
more info
 
S-adenosylmethioninamine metabolic process IEA
Inferred from Electronic Annotation
more info
 
S-adenosylmethionine metabolic process IEA
Inferred from Electronic Annotation
more info
 
aging IEA
Inferred from Electronic Annotation
more info
 
brain development IEA
Inferred from Electronic Annotation
more info
 
cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to lead ion IEA
Inferred from Electronic Annotation
more info
 
cellular response to nerve growth factor stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to platelet-derived growth factor stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to transforming growth factor beta 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
 
neuron differentiation 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
 
response to activity IEA
Inferred from Electronic Annotation
more info
 
response to antidepressant IEA
Inferred from Electronic Annotation
more info
 
response to caffeine IEA
Inferred from Electronic Annotation
more info
 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
response to ethanol IEA
Inferred from Electronic Annotation
more info
 
response to heat IEA
Inferred from Electronic Annotation
more info
 
response to ionizing radiation IEA
Inferred from Electronic Annotation
more info
 
response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
response to testosterone IEA
Inferred from Electronic Annotation
more info
 
response to toxic substance IEA
Inferred from Electronic Annotation
more info
 
response to vitamin A IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
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
 
protein complex 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 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, OTTHUMP00000264207, ENST00000359526, OTTHUMT00000451169
    Conserved Domains (7) summary
    pfam09755
    Location:20237
    DUF2046; Uncharacterized conserved protein H4 (DUF2046)
    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, ENST00000540357
    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, OTTHUMP00000264205, ENST00000340748, 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 details...

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)