Dnmt3l DNA methyltransferase 3-like [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Dnmt3lprovided by MGI
Official Full Name: DNA methyltransferase 3-likeprovided by MGI
Primary source: MGI:MGI:1859287
See related: Ensembl:ENSMUSG00000000730 AllianceGenome:MGI:1859287
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: ecat7; D6Ertd14e
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 that is a catalytically inactive regulatory factor of DNA methyltransferases. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]
Expression: Biased expression in bladder adult (RPKM 7.4), testis adult (RPKM 3.8) and 4 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 C1; 10 39.72 cM

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (77878121..77899456)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (78042287..78063622)

Chromosome 10 - NC_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Extracellular Matrix Stiffness Regulates DNA Methylation by PKCalpha-Dependent Nuclear Transport of DNMT3L.
Title: Extracellular Matrix Stiffness Regulates DNA Methylation by PKCα-Dependent Nuclear Transport of DNMT3L.
Both combinatorial K4me0-K36me3 marks on sister histone H3s of a nucleosome are required for Dnmt3a-Dnmt3L mediated de novo DNA methylation.
Title: Both combinatorial K4me0-K36me3 marks on sister histone H3s of a nucleosome are required for Dnmt3a-Dnmt3L mediated de novo DNA methylation.
The loss of global DNA methylation due to decreased DNMT expression in the postnatal mouse ovaries may associate with infertility emerging during ovarian aging.
Title: The loss of global DNA methylation due to decreased DNMT expression in the postnatal mouse ovaries may associate with infertility emerging during ovarian aging.
NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing.
Title: NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing.
Conversely, monoallelic DNA methylation at imprinted loci was faithfully maintained in all transgenic mice, except H19. Thus, the loci preferred by DNMT3A and DNMT3L differ between somatic and germ cell lineages.
Title: Ectopic expression of DNA methyltransferases DNMT3A2 and DNMT3L leads to aberrant hypermethylation and postnatal lethality in mice.
our work uncovers a role for DNMT3L in maintaining DNMT3A stability, which contributes to the effect of DNMT3L on DNMT3A-dependent DNA methylation
Title: DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells.
The Sirt1 protein suppressed transcription of Dnmt3l.
Title: Sirt1 Regulates DNA Methylation and Differentiation Potential of Embryonic Stem Cells by Antagonizing Dnmt3l.
The Dnmt3l mutation greatly reduced DNA methylation levels at most retrotransposons, but its impact on their RNA abundance was limited in prospermatogonia. In Pld6 mutant germ cells, although only a few retrotransposons exhibited reduced DNA methylation, many showed increased expression at the RNA level.
Title: Switching of dominant retrotransposon silencing strategies from posttranscriptional to transcriptional mechanisms during male germ-cell development in mice.
Dnmt3l-KO donor cells may offer a more permissive epigenetic state that is beneficial for Nuclear transfer reprogramming
Title: Dnmt3l-knockout donor cells improve somatic cell nuclear transfer reprogramming efficiency.
By interacting with TRIM28, DNMT3L can attract various enzymes to form a DNMT3L-induced repressive complex to remove active marks and add repressive marks to histone proteins.
Title: Ectopic DNMT3L triggers assembly of a repressive complex for retroviral silencing in somatic cells.

Submit: New GeneRIF Correction See all GeneRIFs (36)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (8) 1 citation
Endonuclease-mediated (6)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Aire (e-PCR), detects polymorphism
- UniSTS:141058

Dnmt3l (e-PCR), detects polymorphism
- UniSTS:259603

Dnmt3l (e-PCR), detects polymorphism
- UniSTS:467535

NoName (e-PCR)
- UniSTS:548455

RH125967 (e-PCR)
- UniSTS:162679

Dnmt3l (e-PCR), detects polymorphism
- UniSTS:525688

Aire (e-PCR), detects polymorphism
- UniSTS:228479

Dnmt3l (e-PCR), detects polymorphism
- UniSTS:260488

Dnmt3l (e-PCR), detects polymorphism
- UniSTS:260489

D10Jhu43 (e-PCR), detects polymorphism
- UniSTS:158699

Dnmt3l (e-PCR), detects polymorphism
- UniSTS:259069

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
NOT enables DNA (cytosine-5-)-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
NOT enables DNA (cytosine-5-)-methyltransferase activity	IKR Inferred from Key Residues more info	PubMed
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables enzyme activator activity	IBA Inferred from Biological aspect of Ancestor more info
enables enzyme activator activity	IDA Inferred from Direct Assay more info	PubMed
enables enzyme activator activity	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISS Inferred from Sequence or Structural Similarity 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 DNA methylation-dependent heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within autosome genomic imprinting	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chorionic trophoblast cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epigenetic programing of female pronucleus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within genomic imprinting	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in genomic imprinting	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in male meiosis I	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within methylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA methylation-dependent heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression, epigenetic	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression, epigenetic	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within placenta development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retrotransposon silencing by heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrotransposon silencing by heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within spermatogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spermatogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of ESC/E(Z) complex	IDA Inferred from Direct Assay more info	PubMed
part_of catalytic complex	ISO Inferred from Sequence Orthology more info
located_in condensed nuclear chromosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay 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

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_001081695.2 → NP_001075164.1 DNA (cytosine-5)-methyltransferase 3-like isoform 1

See identical proteins and their annotated locations for NP_001075164.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) is expressed in ovary (PMID: 17060371). It differs in the 5' UTR, compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).

Source sequence(s)

AV511576, EF051624

Consensus CDS

CCDS23962.1

UniProtKB/Swiss-Prot

Q9CWR8

UniProtKB/TrEMBL

A3EWM2

Related

ENSMUSP00000121562.2, ENSMUST00000138785.8

Conserved Domains (1) summary

cl22851
Location:81 → 203

PHD_SF; PHD finger superfamily
NM_001284197.1 → NP_001271126.1 DNA (cytosine-5)-methyltransferase 3-like isoform 1

See identical proteins and their annotated locations for NP_001271126.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) is expressed in testis, thymus, ovary, and heart, as well as in 7-day, 15-day, and 17-day embryo (PMID: 11306809). It differs in the 5' UTR, compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).

Source sequence(s)

AF220524, AV473569, AV511576

Consensus CDS

CCDS23962.1

UniProtKB/Swiss-Prot

Q9CWR8

UniProtKB/TrEMBL

A3EWM2

Related

ENSMUSP00000116970.2, ENSMUST00000151242.8

Conserved Domains (1) summary

cl22851
Location:81 → 203

PHD_SF; PHD finger superfamily
NM_001284198.1 → NP_001271127.1 DNA (cytosine-5)-methyltransferase 3-like isoform 2

See identical proteins and their annotated locations for NP_001271127.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) is expressed in testis (PMID: 17060371). It contains alternate 5' UTR exons, lacks a portion of the 5' coding region, and initiates translation at a downstream AUG start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4, 5 and 6 encode the same isoform (2).

Source sequence(s)

AV511576, EF051621

Consensus CDS

CCDS70061.1

UniProtKB/TrEMBL

D3YUQ4

Related

ENSMUSP00000123015.2, ENSMUST00000123940.2
NM_001284199.1 → NP_001271128.1 DNA (cytosine-5)-methyltransferase 3-like isoform 2

See identical proteins and their annotated locations for NP_001271128.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) is expressed in testis (PMID: 17060371). It contains alternate 5' UTR exons, lacks a portion of the 5' coding region, and initiates translation at a downstream AUG start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4, 5 and 6 encode the same isoform (2).

Source sequence(s)

AV511576, EF051622

Consensus CDS

CCDS70061.1

UniProtKB/TrEMBL

D3YUQ4

Related

ENSMUSP00000117827.2, ENSMUST00000139539.8
NM_001284200.1 → NP_001271129.1 DNA (cytosine-5)-methyltransferase 3-like isoform 2

See identical proteins and their annotated locations for NP_001271129.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) is expressed in testis (PMID: 17060371). It contains alternate 5' UTR exons, lacks a portion of the 5' coding region, and initiates translation at a downstream AUG start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1. Variants 4, 5 and 6 encode the same isoform (2).

Source sequence(s)

AV511576, EF051623

Consensus CDS

CCDS70061.1

UniProtKB/TrEMBL

D3YUQ4

Related

ENSMUSP00000119571.2, ENSMUST00000131825.8
NM_019448.4 → NP_062321.1 DNA (cytosine-5)-methyltransferase 3-like isoform 1

See identical proteins and their annotated locations for NP_062321.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) is expressed in prospermatogonia (PMID: 17060371). It encodes the longer isoform (1). Variants 1, 2 and 3 encode the same isoform.

Source sequence(s)

AK010434, AV511576

Consensus CDS

CCDS23962.1

UniProtKB/Swiss-Prot

Q9CWR8

UniProtKB/TrEMBL

A3EWM2

Related

ENSMUSP00000000746.6, ENSMUST00000000746.12

Conserved Domains (1) summary

cl22851
Location:81 → 203

PHD_SF; PHD finger superfamily