dnmt1 DNA (cytosine-5-)-methyltransferase 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: dnmt1provided by ZNC
Official Full Name: DNA (cytosine-5-)-methyltransferase 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-990714-15
See related: Ensembl:ENSDARG00000030756 AllianceGenome:ZFIN:ZDB-GENE-990714-15
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: ddn; mta; cb983; dmnt1; cb1075; fb05h01; wu:fb05h01
Summary: Enables DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates. Involved in DNA methylation and negative regulation of gene expression. Acts upstream of or within several processes, including Kupffer's vesicle development; animal organ development; and macromolecule methylation. Predicted to be active in nucleus. Is expressed in several structures, including digestive system; immature eye; nervous system; neural tube; and tail bud. Human ortholog(s) of this gene implicated in Graves' disease; autosomal dominant cerebellar ataxia, deafness and narcolepsy; hereditary sensory neuropathy; hereditary sensory neuropathy type 1E; and lung non-small cell carcinoma. Orthologous to human DNMT1 (DNA methyltransferase 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: chromosome: 3

Exon count:: 35

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	3	NC_007114.7 (54591218..54607216, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	3	NC_007114.6 (54336616..54352604, complement)

Chromosome 3 - NC_007114.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Rngtt governs biliary-derived liver regeneration initiation by transcriptional regulation of mTORC1 and Dnmt1 in zebrafish.
Title: Rngtt governs biliary-derived liver regeneration initiation by transcriptional regulation of mTORC1 and Dnmt1 in zebrafish.
uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements.
Title: uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements.
dnmt1 function is required to maintain retinal stem cells within the ciliary marginal zone of the zebrafish eye.
Title: dnmt1 function is required to maintain retinal stem cells within the ciliary marginal zone of the zebrafish eye.
the role of Uhrf1 and Dnmt1 in the coordination of intestinal development
Title: Epigenetic factors Dnmt1 and Uhrf1 coordinate intestinal development.
DNMT1 as a potential new small ubiquitin-related modifier-targeted ubiquitin E3 ligase substrate of RNF4, with knockdown of dnmt1 largely restoring primitive and definitive granulopoiesis in rnf4-deficient zebrafish
Title: RNF4 regulates zebrafish granulopoiesis through the DNMT1-C/EBPα axis.
Dnmt1 stability requires UHRF1 phosphorylation and that crosstalk between the proteins is essential for the function of these two important epigenetic regulators during gastrulation
Title: UHRF1 regulation of Dnmt1 is required for pre-gastrula zebrafish development.
Lsh Is Essential for Maintaining Global DNA Methylation Levels in Amphibia and Fish and Interacts Directly with Dnmt1.
Title: Lsh Is Essential for Maintaining Global DNA Methylation Levels in Amphibia and Fish and Interacts Directly with Dnmt1.
Dnmt1 is required for hematopoietic stem and progenitor cells maintenance via cebpa regulation during definitive hematopoiesis in zebrafish
Title: DNA methyltransferase 1 functions through C/ebpa to maintain hematopoietic stem and progenitor cells in zebrafish.
These data provide the first evidence that Uhrf1 and Dnmt1 function is required for vertebrate lens development and maintenance.
Title: Uhrf1 and Dnmt1 are required for development and maintenance of the zebrafish lens.
Thus, our data suggest that Dnmt1 is dispensable for pancreatic duct or endocrine cell formation, but not for acinar cell survival. In addition, Dnmt1 may influence the differentiation of pancreatic beta cell progenitors.
Title: Loss of Dnmt1 catalytic activity reveals multiple roles for DNA methylation during pancreas development and regeneration.

Submit: New GeneRIF Correction See all GeneRIFs (13)

General gene information

Go to the top of the page Help

Markers

fj92b04.y1 (e-PCR)
- UniSTS:200333

fb05h01.x1 (e-PCR)
- UniSTS:189905

fb05h01.x1 (e-PCR)
- UniSTS:189906

mta (e-PCR), detects polymorphism
- UniSTS:205566

Gene Ontology Provided by ZFIN

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	IEA Inferred from Electronic Annotation more info
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within B cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within DNA methylation-dependent heterochromatin formation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within Kupffer's vesicle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within T cell differentiation in thymus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within definitive hemopoiesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within definitive hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of left/right symmetry	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within digestive tract development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epigenetic regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within exocrine pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within granulocyte differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within granulocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within intrahepatic bile duct development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lens development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within liver development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within liver development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retina layer formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retina morphogenesis in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: DNA (cytosine-5)-methyltransferase 1

NP_571264.2

EC 2.1.1.37

XP_017208641.1

EC 2.1.1.37

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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)

NM_131189.2 → NP_571264.2 DNA (cytosine-5)-methyltransferase 1

Status: VALIDATED

Source sequence(s)

CU571160

UniProtKB/TrEMBL

A0A8M1PAS3, F1RCN0

Related

ENSDARP00000013243.3, ENSDART00000021977.5

Conserved Domains (6) summary

COG0270
Location:1022 → 1482

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

cd04711
Location:846 → 982

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:634 → 755

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:525 → 570

zf-CXXC; CXXC zinc finger domain

pfam06464
Location:5 → 95

DMAP_binding; DMAP1-binding Domain

pfam12047
Location:280 → 415

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain