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    RDM1 RNA-DIRECTED DNA METHYLATION 1 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 821839, updated on 18-Sep-2024

    Summary

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    Official Symbol
    RDM1
    Official Full Name
    RNA-DIRECTED DNA METHYLATION 1
    Primary source
    TAIR:AT3G22680
    Locus tag
    AT3G22680
    See related
    Araport:AT3G22680
    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
    RNA-DIRECTED DNA METHYLATION 1
    Summary
    Encodes RNA-DIRECTED DNA METHYLATION 1 (RDM1), forming a complex with DMS3 (AT3G49250) and DRD1 (AT2G16390). This complex is termed DDR. The DDR complex is required for polymerase V transcripts and RNA-directed DNA methylation.
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    Genomic context

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    See RDM1 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    2
    Sequence:
    Chromosome: 3; NC_003074.8 (8017633..8020508)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene F-box and associated interaction domains-containing protein Neighboring gene rRNA processing protein-like protein Neighboring gene Pentatricopeptide repeat (PPR) superfamily protein Neighboring gene LOW protein: PPR containing-like protein Neighboring gene F-box and associated interaction domains-containing 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. Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana. Allard ST, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2005 Jul 1. PMID 16511118, Free PMC Article
    2. The ability to form homodimers is essential for RDM1 to function in RNA-directed DNA methylation. Sasaki T, et al. PLoS One, 2014. PMID 24498436, Free PMC Article
    3. CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation. Wongpalee SP, et al. Nat Commun, 2019 Sep 2. PMID 31477705, Free PMC Article
    4. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Zhong X, et al. Nat Struct Mol Biol, 2012 Sep. PMID 22864289, Free PMC Article
    5. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Gao Z, et al. Nature, 2010 May 6. PMID 20410883, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data show that all DDR complex components DNA-Directed RNA Polymerases (DRD1), defective in meristem silencing 3 (DMS3) and RNA-DIRECTED DNA METHYLATION 1 (RDM1) co-localize with RNA polymerase V (Pol V).
      Title: CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation.
    2. Genome-wide chromatin association of NRPE1 is dependent on all members of a putative chromatin-remodeling complex termed DDR, which includes the proteins DRD1, DMS3 and RDM1.
      Title: DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons.
    3. RDM1 is a component of the RdDM effector complex and may have a role in linking siRNA production with pre-existing or de novo cytosine methylation. [RDM1]
      Title: An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation.
    4. X-ray crystallographic analysis of At3g22680 from Arabidopsis thaliana
      Title: Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana.
    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_113167.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within gene silencing by siRNA-directed DNA methylation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in gene silencing by siRNA-directed DNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in siRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase V complex IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    RNA-DIRECTED DNA METHYLATION 1
    NP_188907.2
    • RNA-DIRECTED DNA METHYLATION 1 (RDM1); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF1950 (InterPro:IPR015270); Has 26 Blast hits to 26 proteins in 8 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 26; Viruses - 0; Other Eukaryotes - 0 (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
      8017633..8020508
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_113167.5 → NP_188907.2  RNA-DIRECTED DNA METHYLATION 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_188907.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q84MD0, Q9LUJ3
      UniProtKB/TrEMBL
      A0A178VFE4, A0A5S9XET6, A0A654FF43
      Conserved Domains (1) summary
      pfam09187
      Location:44 → 162
      RdDM_RDM1; RNA-directed DNA methylation 1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9LUJ3.1

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