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

    Gene ID: 53615, updated on 2-Nov-2024

    Summary

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    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
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    Genomic context

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    See MBD3 in Genome Data Viewer
    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_000019.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 1835 Neighboring gene mex-3 RNA binding family member D Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9728 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9729 Neighboring gene RNA, 7SL, cytoplasmic 477, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:1584307-1584918 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:1584919-1585529 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1590888-1591877 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9734 Neighboring gene ubiquinol-cytochrome c reductase, complex III subunit XI Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1606417-1607038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13618 Neighboring gene RNA, U6 small nuclear 1223, pseudogene Neighboring gene transcription factor 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Methyl-CpG-binding domain 3 inhibits epithelial-mesenchymal transition in pancreatic cancer cells via TGF-β/Smad signalling. Xu M, et al. Br J Cancer, 2017 Jan 3. PMID 27898661, Free PMC Article
    2. Methyl-CpG binding domain protein 3: a new diagnostic marker and potential therapeutic target of melanoma. Ishibashi T, et al. Biosci Trends, 2020 Nov 4. PMID 32963182
    3. Epigenetic programming of the rRNA promoter by MBD3. Brown SE, et al. Mol Cell Biol, 2007 Jul. PMID 17452452, Free PMC Article
    4. DNA demethylation induced by the methyl-CpG-binding domain protein MBD3. Brown SE, et al. Gene, 2008 Sep 1. PMID 18602768
    5. Regulatory landscape and clinical implication of MBD3 in human malignant glioma. Cui Y, et al. Oncotarget, 2016 Dec 6. PMID 27835581, Free PMC Article

    See all (172) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ35189, DKFZp762G113

    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 PubMed 
    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
    		  
    involved_in chromatin remodeling HDA 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 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 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

    1. NG_029897.3 RefSeqGene

      Range
      5000..24269
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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

    2. 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

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      1573596..1592865 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      1544415..1563688 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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

    1. 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.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95983.1 GenPept UniProtKB/Swiss-Prot:O95983

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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