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    MBD9 methyl-CPG-binding domain 9 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 821132, updated on 18-Sep-2024

    Summary

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    Official Symbol
    MBD9
    Official Full Name
    methyl-CPG-binding domain 9
    Primary source
    TAIR:AT3G01460
    Locus tag
    AT3G01460
    See related
    Araport:AT3G01460
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    ATMBD9; methyl-CPG-binding domain 9; T13O15.10; T13O15_10
    Summary
    Encodes a protein with a methyl-CpG-binding domain. Has sequence similarity to human MBD proteins. Involved in the modification of the FLC chromatin acetylation state to affect FLC expression. Mutants show an early flowering, and enhanced shoot branching phenotypes.
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    Genomic context

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    See MBD9 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    10
    Sequence:
    Chromosome: 3; NC_003074.8 (173190..182454)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene NHL domain protein Neighboring gene uncharacterized protein Neighboring gene ARM repeat superfamily protein Neighboring gene PsbQ-like 1 Neighboring gene ncRNA Neighboring gene uncharacterized protein Neighboring gene homeobox 1 Neighboring gene cyclophilin 38 Neighboring gene Protein kinase superfamily protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome. Sijacic P, et al. PLoS Genet, 2019 Aug. PMID 31381567, Free PMC Article
    2. AtMBD9: a protein with a methyl-CpG-binding domain regulates flowering time and shoot branching in Arabidopsis. Peng M, et al. Plant J, 2006 Apr. PMID 16623890
    3. Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. Potok ME, et al. Nat Commun, 2019 Jul 26. PMID 31350403, Free PMC Article
    4. AtMBD9 modulates Arabidopsis development through the dual epigenetic pathways of DNA methylation and histone acetylation. Yaish MW, et al. Plant J, 2009 Jul. PMID 19419532
    5. Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. Zemach A, et al. Plant J, 2003 Jun. PMID 12787239

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Methyl-CpG-BINDING DOMAIN 9 (MBD9), is required for H2A.Z incorporation at thousands of genomic sites that share a distinct histone modification profile. The histone binding properties of MBD9 suggest that it may guide H2A.Z deposition to specific sites by interacting with modified nucleosomes and with the H2A.Z deposition complex.
      Title: Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome.
    2. MBD9 is a SWR1-C interacting protein required for H2A.Z deposition at a subset of actively transcribing genes.
      Title: Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition.
    3. AtMBD9 controls flowering time and axillary branching by modulating gene expression through DNA methylation and histone acetylation.
      Title: AtMBD9 modulates Arabidopsis development through the dual epigenetic pathways of DNA methylation and histone acetylation.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_111012.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables histone acetyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables methyl-CpG binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in epigenetic regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within photoperiodism, flowering IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within secondary shoot formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Swr1 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    located_in plasmodesma HDA PubMed 

    General protein information

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    Preferred Names
    methyl-CPG-binding domain 9
    NP_186795.1
    • methyl-CPG-binding domain 9 (MBD9); FUNCTIONS IN: methyl-CpG binding, DNA binding; INVOLVED IN: photoperiodism, flowering, secondary shoot formation, regulation of transcription, DNA-dependent; LOCATED IN: nucleus; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, RING-type (InterPro:IPR001841), FY-rich, C-terminal (InterPro:IPR003889), Zinc finger, PHD-type (InterPro:IPR001965), FY-rich, N-terminal (InterPro:IPR003888), DNA-binding, integrase-type (InterPro:IPR016177), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Methyl-CpG DNA binding (InterPro:IPR001739), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: RING/FYVE/PHD-type zinc finger family protein (TAIR:AT1G77250.1); Has 6416 Blast hits to 3988 proteins in 224 species: Archae - 0; Bacteria - 0; Metazoa - 4085; Fungi - 602; Plants - 1260; Viruses - 0; Other Eukaryotes - 469 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003074.8 Reference assembly

      Range
      173190..182454
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_111012.4 → NP_186795.1  methyl-CPG-binding domain 9 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_186795.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9SGH2, Q9SSA6
      UniProtKB/TrEMBL
      A0A178VJY9, A0A5S9X859, A0A654F351
      Conserved Domains (6) summary
      cd15519
      Location:1289 → 1334
      PHD1_Lid2p_like; PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins
      pfam01429
      Location:258 → 311
      MBD; Methyl-CpG binding domain
      cl02608
      Location:1312 → 1390
      BAH; or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...
      cl02650
      Location:413 → 453
      FYRN; F/Y-rich N-terminus
      cl02651
      Location:671 → 695
      FYRC; F/Y rich C-terminus
      cl22851
      Location:86 → 130
      PHD_SF; PHD finger superfamily
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9SGH2.1

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