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

Summary

Official Symbol: DNMT1provided by HGNC
Official Full Name: DNA methyltransferase 1provided by HGNC
Primary source: HGNC:HGNC:2976
See related: Ensembl:ENSG00000130816 MIM:126375; AllianceGenome:HGNC:2976
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: mouse all
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Genomic context

Location:: 19p13.2

Exon count:: 41

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (10133346..10194953, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (10259569..10321116, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (10244022..10305629, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Obesity promotes the global hypomethylation of CD4+ T cells in patients with systemic lupus erythematosus via downregulating DNMT1.
Title: Obesity promotes the global hypomethylation of CD4+ T cells in patients with systemic lupus erythematosus via downregulating DNMT1.
DNMT1-Mediated the Downregulation of FOXF1 Promotes High Glucose-induced Podocyte Damage by Regulating the miR-342-3p/E2F1 Axis.
Title: DNMT1-Mediated the Downregulation of FOXF1 Promotes High Glucose-induced Podocyte Damage by Regulating the miR-342-3p/E2F1 Axis.
LncRNA FAM83H-AS1 inhibits ferroptosis of endometrial cancer by promoting DNMT1-mediated CDO1 promoter hypermethylation.
Title: LncRNA FAM83H-AS1 inhibits ferroptosis of endometrial cancer by promoting DNMT1-mediated CDO1 promoter hypermethylation.
Genome-wide CRISPR-Cas9 knockout screens identify DNMT1 as a druggable dependency in sonic hedgehog medulloblastoma.
Title: Genome-wide CRISPR-Cas9 knockout screens identify DNMT1 as a druggable dependency in sonic hedgehog medulloblastoma.
DNMT1 regulates human erythropoiesis by modulating cell cycle and endoplasmic reticulum stress in a stage-specific manner.
Title: DNMT1 regulates human erythropoiesis by modulating cell cycle and endoplasmic reticulum stress in a stage-specific manner.
Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy.
Title: Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy.
DNMT1-targeting remodeling global DNA hypomethylation for enhanced tumor suppression and circumvented toxicity in oral squamous cell carcinoma.
Title: DNMT1-targeting remodeling global DNA hypomethylation for enhanced tumor suppression and circumvented toxicity in oral squamous cell carcinoma.
Role of LINC00240 on T-helper 9 differentiation in allergic rhinitis through influencing DNMT1-dependent methylation of PU.1.
Title: Role of LINC00240 on T-helper 9 differentiation in allergic rhinitis through influencing DNMT1-dependent methylation of PU.1.
An updated meta-analysis investigating the association between DNMTs gene polymorphism andgastric cancer risk.
Title: An updated meta-analysis investigating the association between DNMTs gene polymorphism andgastric cancer risk.
Unveiling the impact of DNA methylation machinery: Dnmt1 and Dnmt3a in orchestrating oocyte development and cellular homeostasis.
Title: Unveiling the impact of DNA methylation machinery: Dnmt1 and Dnmt3a in orchestrating oocyte development and cellular homeostasis.

Submit: New GeneRIF Correction See all GeneRIFs (614)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal dominant cerebellar ataxia, deafness and narcolepsy MedGen: C3807295 OMIM: 604121 GeneReviews: Not available	Compare labs
Hereditary sensory neuropathy-deafness-dementia syndrome MedGen: C3279885 OMIM: 614116 GeneReviews: Charcot-Marie-Tooth Hereditary Neuropathy Overview, DNMT1-Related Disorder	Compare labs

EBI 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. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH18124 (e-PCR)
- UniSTS:42581

D19S830 (e-PCR)
- UniSTS:32498

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA (cytosine-5-)-methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA (cytosine-5-)-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables lncRNA binding	IEA Inferred from Electronic Annotation more info
enables methyl-CpG binding	IEA Inferred from Electronic Annotation more info
enables promoter-specific chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent heterochromatin formation	IEA Inferred from Electronic Annotation more info
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in cellular response to amino acid stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to bisphenol A	IEA Inferred from Electronic Annotation more info
involved_in chromosomal DNA methylation maintenance following DNA replication	TAS Traceable Author Statement more info	PubMed
involved_in epigenetic programming of gene expression	IEA Inferred from Electronic Annotation more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression via chromosomal CpG island methylation	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of vascular associated smooth muscle cell apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of vascular associated smooth muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in female germ cell nucleus	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	HTP more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in pericentric heterochromatin	IEA Inferred from Electronic Annotation more info
located_in replication fork	IEA Inferred from Electronic Annotation more info

General protein information

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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

EC 2.1.1.37

NP_001305659.1

EC 2.1.1.37

NP_001305660.1

EC 2.1.1.37

NP_001370.1

EC 2.1.1.37

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.

Genomic

NG_028016.3 RefSeqGene

Range

41208..102941

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_362

mRNA and Protein(s)

NM_001130823.3 → NP_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, X63692

Consensus CDS

CCDS45958.1

UniProtKB/TrEMBL

Q59FP7

Related

ENSP00000352516.3, ENST00000359526.9

Conserved Domains (6) summary

COG0270
Location:1154 → 1608

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

cd04711
Location:981 → 1117

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:770 → 893

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:661 → 707

zf-CXXC; CXXC zinc finger domain

pfam06464
Location:16 → 105

DMAP_binding; DMAP1-binding Domain

pfam12047
Location:415 → 550

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
NM_001318730.2 → NP_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/TrEMBL

Q59FP7

Related

ENSP00000504512.1, ENST00000679313.1

Conserved Domains (6) summary

COG0270
Location:1138 → 1595

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

cd04711
Location:965 → 1101

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:754 → 877

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:645 → 691

zf-CXXC; CXXC zinc finger domain

pfam06464
Location:16 → 105

DMAP_binding; DMAP1-binding Domain

pfam12047
Location:399 → 534

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
NM_001318731.2 → NP_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, X63692

UniProtKB/TrEMBL

I6L9H2, Q59FP7

Conserved Domains (5) summary

COG0270
Location:1033 → 1487

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

cd04711
Location:860 → 996

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:649 → 772

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:540 → 586

zf-CXXC; CXXC zinc finger domain

pfam12047
Location:294 → 429

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain
NM_001379.4 → NP_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, X63692

Consensus CDS

CCDS12228.1

UniProtKB/Swiss-Prot

A0AV63, B7ZLW6, P26358, Q9UHG5, Q9ULA2, Q9UMZ6

UniProtKB/TrEMBL

Q59FP7

Related

ENSP00000345739.3, ENST00000340748.8

Conserved Domains (6) summary

COG0270
Location:1138 → 1592

Dcm; Site-specific DNA-cytosine methylase [Replication, recombination and repair]

cd04711
Location:965 → 1101

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:754 → 877

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:645 → 691

zf-CXXC; CXXC zinc finger domain

pfam06464
Location:16 → 105

DMAP_binding; DMAP1-binding Domain

pfam12047
Location:399 → 534

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain