DNMT3L DNA methyltransferase 3 like [Homo sapiens (human)] - Gene

Summary

Official Symbol: DNMT3Lprovided by HGNC
Official Full Name: DNA methyltransferase 3 likeprovided by HGNC
Primary source: HGNC:HGNC:2980
See related: Ensembl:ENSG00000142182 MIM:606588; AllianceGenome:HGNC:2980
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: CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a nuclear protein with similarity to DNA methyltransferases, but is not thought to function as a DNA methyltransferase as it does not contain the amino acid residues necessary for methyltransferase activity. However, it does stimulate de novo methylation by DNA cytosine methyltransferase 3 alpha and is thought to be required for the establishment of maternal genomic imprints. This protein also mediates transcriptional repression through interaction with histone deacetylase 1. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]
Expression: Biased expression in liver (RPKM 1.3), kidney (RPKM 1.0) and 3 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 21q22.3

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	21	NC_000021.9 (44246339..44261897, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	21	NC_060945.1 (42600400..42615957, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	21	NC_000021.8 (45666222..45681780, complement)

Chromosome 21 - NC_000021.9 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
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?

Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature.
Title: Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature.
Decoding the Genetic Alterations in Genes of DNMT Family (DNA Methyl-Transferase) and their Association with Head and Neck Squamous Cell Carcinoma.
Title: Decoding the Genetic Alterations in Genes of DNMT Family (DNA Methyl-Transferase) and their Association with Head and Neck Squamous Cell Carcinoma.
EGR1 interacts with DNMT3L to inhibit the transcription of miR-195 and plays an anti-apoptotic role in the development of gastric cancer.
Title: EGR1 interacts with DNMT3L to inhibit the transcription of miR-195 and plays an anti-apoptotic role in the development of gastric cancer.
Nutrition and its DNA methylation influence cognitive decline.
Title: Interaction of nutrition and genetics via DNMT3L-mediated DNA methylation determines cognitive decline.
DNMT3L overexpression is associated with Down syndrome.
Title: Global hypermethylation in fetal cortex of Down syndrome due to DNMT3L overexpression.
the present study has demonstrated that variations in the DNMT3L gene do not contribute to stage I-II endometriosis-associated infertility.
Title: Association between DNMT3L polymorphic variants and the risk of endometriosis-associated infertility.
DNMT3L rs2070565 (genotype P = 0.007, allele P = 0.0026) confers an increased risk of developing schizophrenia at an early age in individuals with family history.
Title: DNA methyl transferase (DNMT) gene polymorphisms could be a primary event in epigenetic susceptibility to schizophrenia.
crystal structures of DNMT3A-DNMT3L (autoinhibitory form) and DNMT3A-DNMT3L-H3 (active form) complexes at 3.82 and 2.90 A resolution, respectively
Title: Structural insight into autoinhibition and histone H3-induced activation of DNMT3A.
DNMT3L can address DNMT3A/B to specific sites by directly interacting with TFs that do not directly interact with DNMT3A/B
Title: DNMT3L interacts with transcription factors to target DNMT3L/DNMT3B to specific DNA sequences: role of the DNMT3L/DNMT3B/p65-NFκB complex in the (de-)methylation of TRAF1.
CpG island encompassing the promoter and first exon of human DNMT3L gene is a PcG/TrX response element
Title: The CpG island encompassing the promoter and first exon of human DNMT3L gene is a PcG/TrX response element (PRE).

Submit: New GeneRIF Correction See all GeneRIFs (33)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Homologs of the DNMT3L gene: The DNMT3L gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, and rat.
Orthologs from Annotation Pipeline: 224 organisms have orthologs with human gene DNMT3L
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables enzyme activator activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables enzyme activator activity	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in C-5 methylation of cytosine	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in C-5 methylation of cytosine	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA methylation	NAS Non-traceable Author Statement more info	PubMed
involved_in DNA methylation involved in gamete generation	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA methylation on cytosine	ISS Inferred from Sequence or Structural Similarity more info
involved_in chorionic trophoblast cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in genomic imprinting	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in male meiosis I	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA methylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of transposition	IEA Inferred from Electronic Annotation more info
involved_in placenta development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA methylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of gene expression by genomic imprinting	NAS Non-traceable Author Statement more info	PubMed
involved_in spermatogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in spermatogenesis	NAS Non-traceable Author Statement more info	PubMed
involved_in stem cell differentiation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of catalytic complex	IPI Inferred from Physical Interaction more info	PubMed
located_in condensed nuclear chromosome	IEA Inferred from Electronic Annotation more info
located_in cytosol	HDA more info	PubMed
located_in heterochromatin	IEA Inferred from Electronic Annotation more info
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: DNA (cytosine-5)-methyltransferase 3-like

Names: DNA (cytosine-5-)-methyltransferase 3-like; cytosine-5-methyltransferase 3-like protein; human cytosine-5-methyltransferase 3-like protein

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)

NM_013369.4 → NP_037501.2 DNA (cytosine-5)-methyltransferase 3-like isoform 1

See identical proteins and their annotated locations for NP_037501.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AF194032, BC002560, BQ028660

Consensus CDS

CCDS13705.1

UniProtKB/Swiss-Prot

Q9UJW3

Related

ENSP00000270172.3, ENST00000270172.7

Conserved Domains (1) summary

cl22851
Location:47 → 169

PHD_SF; PHD finger superfamily
NM_175867.3 → NP_787063.1 DNA (cytosine-5)-methyltransferase 3-like isoform 2

See identical proteins and their annotated locations for NP_787063.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site at the 3' terminal exon compared to variant 1, which results in an isoform (2) that is 1 aa shorter than isoform 1.

Source sequence(s)

AF194032, BC002560, BQ028660

Consensus CDS

CCDS46650.1

UniProtKB/Swiss-Prot

Q9BUJ4, Q9UJW3

Related

ENSP00000486001.1, ENST00000628202.3

Conserved Domains (1) summary

cl22851
Location:47 → 169

PHD_SF; PHD finger superfamily