Mbd3 methyl-CpG binding domain protein 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Mbd3provided by MGI
Official Full Name: methyl-CpG binding domain protein 3provided by MGI
Primary source: MGI:MGI:1333812
See related: Ensembl:ENSMUSG00000035478 AllianceGenome:MGI:1333812
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
Summary: This gene encodes a member of the MBD family of nuclear proteins that contain a methyl-CpG binding domain (MBD). The encoded protein is a component of the nucleosome remodeling and histone deacetylation (NuRD) complex. Deletion of this gene causes embryonic lethality in mice. Embryonic stem cells lacking the encoded protein are severely compromised in their ability to differentiate and fail to commit to developmental lineages in the absence of leukemia inhibitory factor. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 83.1), ovary adult (RPKM 79.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 C1; 10 39.72 cM

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (80228373..80235365, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (80392539..80399531, complement)

Chromosome 10 - NC_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

Expression of mBD4, mBD3 and CRAMP during type II collagen-induced arthritis/CIA and their association with inflammation and bone-remodeling markers.
Title: Expression of mBD4, mBD3 and CRAMP during type II collagen-induced arthritis/CIA and their association with inflammation and bone-remodeling markers.
Analyses also revealed that the coiled-coil domain common to all three MBD3 isoforms, but not the MBD domain, plays a crucial role in this activity.
Title: Identification of the Coiled-Coil Domain as an Essential Methyl-CpG-Binding Domain Protein 3 Element for Preserving Lineage Commitment Potential of Embryonic Stem Cells.
It validates a distinct molecular axis, Gatad2a-Chd4-Mbd3, within Mbd3/NuRD as being critical for blocking reestablishment of naive pluripotency and further highlight signaling-dependent and post-translational modifications of Mbd3/NuRD that influence its interactions and assembly.
Title: Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency.
It has been shown that chromatin localization of Mbd2 and Mbd3 is highly overlapping, and both proteins are interdependent for chromatin association.
Title: DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells.
controls lymphoid cell fate and inhibits tumorigenesis by repressing a B cell transcriptional program
Title: Mbd3/NuRD controls lymphoid cell fate and inhibits tumorigenesis by repressing a B cell transcriptional program.
Smek/Mbd3 interaction regulates neuronal gene expression and neuronal differentiation during cortical development.
Title: Smek promotes corticogenesis through regulating Mbd3's stability and Mbd3/NuRD complex recruitment to genes associated with neurogenesis.
This work revealed the critical function of miR-134-Mbd3 axis on regulating reprogramming and pluripotency of induced pluripotent stem cells derived from the neural progenitor cells.
Title: MiR-134-Mbd3 axis regulates the induction of pluripotency.
Cigarette smoke induces proteosomal-mediated degradation of Mbd-3 in embryonic orofacial cells.
Title: Cigarette smoke induces proteasomal-mediated degradation of DNA methyltransferases and methyl CpG-/CpG domain-binding proteins in embryonic orofacial cells.
Although MBD3/NuRD is not required for neural stem cell lineage commitment, it is required to repress inappropriate transcription in progenitor cells and neurons to facilitate appropriate cell lineage choice and differentiation programmes.
Title: The methyl binding domain 3/nucleosome remodelling and deacetylase complex regulates neural cell fate determination and terminal differentiation in the cerebral cortex.
overexpression facilitates NANOG-mediated reprogramming in neural stem cells
Title: MBD3/NuRD facilitates induction of pluripotency in a context-dependent manner.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Variation

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Alleles

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

Gene trapped (1)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH136543 (e-PCR)
- UniSTS:210525

Mbd3 (e-PCR), detects polymorphism
- UniSTS:498797

Mbd3 (e-PCR), detects polymorphism
- UniSTS:525694

RH126839 (e-PCR)
- UniSTS:208574

Mbd3 (e-PCR), detects polymorphism
- UniSTS:143836

RH135907 (e-PCR)
- UniSTS:209905

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info
enables methyl-CpG binding	IBA Inferred from Biological aspect of Ancestor more info
enables methyl-CpG binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within DNA methylation-dependent heterochromatin formation	IDA Inferred from Direct Assay more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	NAS Non-traceable Author Statement 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 negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info
involved_in positive regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of cell fate specification	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of stem cell differentiation	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within tissue development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of NuRD complex	IPI Inferred from Physical Interaction more info	PubMed
part_of NuRD complex	ISO Inferred from Sequence Orthology more info
part_of NuRD complex	NAS Non-traceable Author Statement more info	PubMed
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of heterochromatin	IDA Inferred from Direct Assay more info	PubMed
NOT located_in nucleolus	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
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: methyl-CpG-binding domain protein 3

Names: methyl-CpG-binding protein MBD3

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_001306143.1 → NP_001293072.1 methyl-CpG-binding domain protein 3 isoform 2

See identical proteins and their annotated locations for NP_001293072.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. It encodes isoform 2 which has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AC152062, BP770230, BQ042794, CK625083

Consensus CDS

CCDS78860.1

UniProtKB/TrEMBL

D3YTR5

Related

ENSMUSP00000100986.2, ENSMUST00000105349.8

Conserved Domains (3) summary

pfam14048
Location:121 → 211

MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3

pfam16564
Location:51 → 116

MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD

cl00110
Location:5 → 47

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...
NM_013595.3 → NP_038623.1 methyl-CpG-binding domain protein 3 isoform 1

See identical proteins and their annotated locations for NP_038623.1

Status: REVIEWED

Description

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

Source sequence(s)

AC152062, BP770230, BQ042794, CK625083, CX208033

Consensus CDS

CCDS24020.1

UniProtKB/Swiss-Prot

Q792D3, Q8CFJ1, Q9Z2D8

UniProtKB/TrEMBL

D3YTR5

Related

ENSMUSP00000089948.4, ENSMUST00000092295.10

Conserved Domains (3) summary

cd01396
Location:5 → 79

MeCP2_MBD; MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding ...

pfam14048
Location:153 → 243

MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3

pfam16564
Location:83 → 148

MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD