MBD3 methyl-CpG binding domain protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: MBD3provided by HGNC
Official Full Name: methyl-CpG binding domain protein 3provided by HGNC
Primary source: HGNC:HGNC:6918
See related: Ensembl:ENSG00000071655 MIM:603573; AllianceGenome:HGNC:6918
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: DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. This gene belongs to a family of nuclear proteins which are characterized by the presence of a methyl-CpG binding domain (MBD). The encoded protein is a subunit of the NuRD, a multisubunit complex containing nucleosome remodeling and histone deacetylase activities. Unlike the other family members, the encoded protein is not capable of binding to methylated DNA. The protein mediates the association of metastasis-associated protein 2 with the core histone deacetylase complex. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]
Expression: Ubiquitous expression in placenta (RPKM 23.4), fat (RPKM 18.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (1573596..1592865, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (1544415..1563688, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (1573595..1592864, 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?

Densely methylated DNA traps Methyl-CpG-binding domain protein 2 but permits free diffusion by Methyl-CpG-binding domain protein 3.
Title: Densely methylated DNA traps Methyl-CpG-binding domain protein 2 but permits free diffusion by Methyl-CpG-binding domain protein 3.
MBD3 promotes hepatocellular carcinoma progression and metastasis through negative regulation of tumour suppressor TFPI2.
Title: MBD3 promotes hepatocellular carcinoma progression and metastasis through negative regulation of tumour suppressor TFPI2.
Methyl-CpG binding domain protein 3: a new diagnostic marker and potential therapeutic target of melanoma.
Title: Methyl-CpG binding domain protein 3: a new diagnostic marker and potential therapeutic target of melanoma.
Glioma stem-like cells evade interferon suppression through MBD3/NuRD complex-mediated STAT1 downregulation.
Title: Glioma stem-like cells evade interferon suppression through MBD3/NuRD complex-mediated STAT1 downregulation.
Histone deacetylases, Mbd3/NuRD, and Tet2 hydroxylase are crucial regulators of epithelial-mesenchymal plasticity and tumor metastasis.
Title: Histone deacetylases, Mbd3/NuRD, and Tet2 hydroxylase are crucial regulators of epithelial-mesenchymal plasticity and tumor metastasis.
our results demonstrate that mCG-binding arginine fingers embedded into a conserved structural fold are essential structural features for MBD2/3s binding to methylated DNA among metazoans.
Title: Structural analyses reveal that MBD3 is a methylated CG binder.
the interplay of the Zalpha domain from ADAR1 and MBD3 may regulate the transition of the DNA conformation between B- and Z-DNA and thereby modulate chromatin accessibility, resulting in alterations in gene expression
Title: The C-terminal D/E-rich domain of MBD3 is a putative Z-DNA mimic that competes for Zα DNA-binding activity.
Study have demonstrated that MBD3/ NuRD inhibits formation of liver induced cancer stem cells (iCSCs). In addition, MBD3 suppression induces c-JUN, resulting in the induction of pluripotent genes in iCSCs.
Title: MBD3 inhibits formation of liver cancer stem cells.
Suggest that MBD3 exerts influences on both active and silenced genes in glioma cells.
Title: Regulatory landscape and clinical implication of MBD3 in human malignant glioma.
MBD3 inhibits epithelial-mesenchymal transition in pancreatic cancer cells probably via TGF-beta/Smad signaling and may be a candidate for diagnostics and prognosis of pancreatic cancer.
Title: Methyl-CpG-binding domain 3 inhibits epithelial-mesenchymal transition in pancreatic cancer cells via TGF-β/Smad signalling.

Submit: New GeneRIF Correction See all GeneRIFs (27)

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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Markers

D1S281E (e-PCR)
- UniSTS:147394

MBD3 (e-PCR)
- UniSTS:278722

RH91108 (e-PCR)
- UniSTS:92413

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	TAS Traceable Author Statement more info	PubMed
enables methyl-CpG binding	IBA Inferred from Biological aspect of Ancestor more info
enables methyl-CpG binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to nucleosomal DNA binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent constitutive heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	HDA more info	PubMed
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in embryonic organ development	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
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
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
involved_in response to estradiol	IEA Inferred from Electronic Annotation more info
involved_in response to nutrient levels	IEA Inferred from Electronic Annotation more info
involved_in ventricular cardiac muscle tissue development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of NuRD complex	IDA Inferred from Direct Assay more info	PubMed
part_of NuRD complex	NAS Non-traceable Author Statement more info	PubMed
located_in chromatin	HDA more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in heterochromatin	IEA Inferred from Electronic Annotation more info
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
part_of protein-containing complex	HDA more info	PubMed

General protein information

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Preferred Names: methyl-CpG-binding domain protein 3

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_029897.3 RefSeqGene

Range

5000..24269

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001281453.2 → NP_001268382.1 methyl-CpG-binding domain protein 3 isoform 1

See identical proteins and their annotated locations for NP_001268382.1

Status: REVIEWED

Description

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

Source sequence(s)

AC005943

Consensus CDS

CCDS12072.1

UniProtKB/Swiss-Prot

A8K4B7, D6W5Z2, O95983, Q6PIL9, Q6PJZ9, Q86XF4

Related

ENSP00000412302.2, ENST00000434436.8

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:82 → 148

MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD
NM_001281454.2 → NP_001268383.1 methyl-CpG-binding domain protein 3 isoform 2

See identical proteins and their annotated locations for NP_001268383.1

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 lacks an internal segment and is shorter, compared to isoform 1.

Source sequence(s)

AC005943

Consensus CDS

CCDS62481.1

UniProtKB/TrEMBL

B3KMA8

Related

ENSP00000156825.2, ENST00000156825.5

Conserved Domains (3) summary

pfam14048
Location:121 → 211

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

pfam16564
Location:50 → 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 ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

1573596..1592865 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047438939.1 → XP_047294895.1 methyl-CpG-binding domain protein 3 isoform X1

UniProtKB/Swiss-Prot

A8K4B7, D6W5Z2, O95983, Q6PIL9, Q6PJZ9, Q86XF4

Related

ENSP00000464718.1, ENST00000590550.6

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

1544415..1563688 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054321223.1 → XP_054177198.1 methyl-CpG-binding domain protein 3 isoform X1

UniProtKB/Swiss-Prot

A8K4B7, D6W5Z2, O95983, Q6PIL9, Q6PJZ9, Q86XF4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_003926.5: Suppressed sequence

Description

NM_003926.5: This RefSeq was permanently suppressed because currently there is support for the protein but not for the transcript.