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    NRPD1A nuclear RNA polymerase D1A [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 842605, updated on 18-Sep-2024

    Summary

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    Official Symbol
    NRPD1A
    Official Full Name
    nuclear RNA polymerase D1A
    Primary source
    TAIR:AT1G63020
    Locus tag
    AT1G63020
    See related
    Araport:AT1G63020
    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
    F16P17.19; F16P17_19; NRPD1; NUCLEAR RNA POLYMERASE D 1A; nuclear RNA polymerase D1A; POL IVA; SDE4; SILENCING MOVEMENT DEFICIENT 2; SMD2
    Summary
    Encodes one of two alternative largest subunits of a putative plant-specific RNA polymerase IV (aka RNA polymerase D). Required for posttranscriptional gene silencing.
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    Genomic context

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    See NRPD1A in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    20
    Sequence:
    Chromosome: 1; NC_003070.9 (23354685..23362589, complement)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene Major Facilitator Superfamily with SPX (SYG1/Pho81/XPR1) domain-containing protein Neighboring gene ncRNA Neighboring gene Integrase-type DNA-binding superfamily protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The NRPD1 N-terminus contains a Pol IV-specific motif that is critical for genome surveillance in Arabidopsis. Ferrafiat L, et al. Nucleic Acids Res, 2019 Sep 26. PMID 31372633, Free PMC Article
    2. The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation. Wendte JM, et al. Nucleic Acids Res, 2019 Sep 26. PMID 31329950, Free PMC Article
    3. Maternal control of Pol IV-dependent siRNAs in Arabidopsis endosperm. Mosher RA. New Phytol, 2010 Apr. PMID 20074090
    4. Role of RNA polymerase IV in plant small RNA metabolism. Zhang X, et al. Proc Natl Acad Sci U S A, 2007 Mar 13. PMID 17360559, Free PMC Article
    5. RNA polymerases IV and V influence the 3' boundaries of Polymerase II transcription units in Arabidopsis. McKinlay A, et al. RNA Biol, 2018 Feb 1. PMID 29199514, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The C-terminal domain is dispensable for Pol IV catalytic activity and Pol IV termination-dependent activation of RNA-DEPENDENT RNA POLYMERASE 2, which partners with Pol IV to generate dsRNA precursors of the 24 nt siRNAs that guide RdDM.
      Title: The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation.
    2. The NRPD1 N-terminus is critical for robust Pol IV-dependent transcription, siRNA production and DNA methylation.
      Title: The NRPD1 N-terminus contains a Pol IV-specific motif that is critical for genome surveillance in Arabidopsis.
    3. Results show that although Pols IV and V are detected near transcript ends of the affected Pol II - transcribed genes, their role in limiting Pol II read-through is independent of siRNA biogenesis or cytosine methylation for the majority of these genes. The splicing was less efficient in pol IV or pol V mutant plants, compared to wild-type, suggesting that Pol IV or Pol V might affect pre-mRNA processing. [POL IV]
      Title: RNA polymerases IV and V influence the 3' boundaries of Polymerase II transcription units in Arabidopsis.
    4. The authors identified Pol IV and RDR2-dependent RNAs (P4R2 RNAs) that accumulate in dcl3 mutants and are diced into 24 nt RNAs by DCL3 in vitro.
      Title: Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis.
    5. Data show that SHH1(AT1G15215), RDR2, CLASSY1, and RDM4 were co-purified with NRPD1(At1g63020), the largest subunit of Pol-IV.
      Title: SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.
    6. Pol IV-dependent (p4-)siRNAs are initially expressed in the maternal gametophyte and uniparentally expressed from maternal chromosomes in developing endosperm.
      Title: Maternal control of Pol IV-dependent siRNAs in Arabidopsis endosperm.
    7. Arabidopsis Pol II is indispensable for endogenous siRNA-mediated transcriptional gene silencing (TGS) at intergenic low-copy-number loci, despite the presence of two other polymerases-Pol IV and Pol V-that specialize in TGS through siRNAs
      Title: Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis.
    8. Mutants defective for the NRPD1a and NRPD1b alternative largest subunits of polymerase IV were tested for their ability to undergo RNA silencing and mantenance of transcription and post-transcriptional silencing
      Title: NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis.
    9. NRPD1a is required for reception of long-distance mRNA silencing.
      Title: Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis.
    10. RNA polymerase IV has a role in plant small RNA metabolism [RNAP IV]
      Title: Role of RNA polymerase IV in plant small RNA metabolism.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001198369.1
    NM_001334063.1
    NM_104980.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-directed 5'-3' RNA polymerase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulatory ncRNA-mediated gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within siRNA processing IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within siRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within siRNA-mediated long-distance post-transcriptional gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase IV complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm 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
    		  

    General protein information

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    Preferred Names
    nuclear RNA polymerase D1A
    NP_001185298.1
    • nuclear RNA polymerase D1A (NRPD1A); FUNCTIONS IN: DNA-directed RNA polymerase activity, DNA binding; INVOLVED IN: in 7 processes; LOCATED IN: nucleus, DNA-directed RNA polymerase IV complex; EXPRESSED IN: 9 plant structures; EXPRESSED DURING: 6 growth stages; CONTAINS InterPro DOMAIN/s: RNA polymerase, N-terminal (InterPro:IPR006592), RNA polymerase, alpha subunit (InterPro:IPR000722), RNA polymerase Rpb1, domain 3 (InterPro:IPR007066), RNA polymerase Rpb1, domain 1 (InterPro:IPR007080), RNA polymerase Rpb1, domain 4 (InterPro:IPR007083), Protein of unknown function DUF3223 (InterPro:IPR021602), RNA polymerase Rpb1, domain 5 (InterPro:IPR007081); BEST Arabidopsis thaliana protein match is: nuclear RNA polymerase D1B (TAIR:AT2G40030.1).
    NP_176490.2
    • nuclear RNA polymerase D1A (NRPD1A); FUNCTIONS IN: DNA-directed RNA polymerase activity, DNA binding; INVOLVED IN: in 7 processes; LOCATED IN: nucleus, DNA-directed RNA polymerase IV complex; EXPRESSED IN: 9 plant structures; EXPRESSED DURING: 6 growth stages; CONTAINS InterPro DOMAIN/s: RNA polymerase, N-terminal (InterPro:IPR006592), RNA polymerase, alpha subunit (InterPro:IPR000722), RNA polymerase Rpb1, domain 3 (InterPro:IPR007066), RNA polymerase Rpb1, domain 1 (InterPro:IPR007080), RNA polymerase Rpb1, domain 4 (InterPro:IPR007083), Protein of unknown function DUF3223 (InterPro:IPR021602), RNA polymerase Rpb1, domain 5 (InterPro:IPR007081); BEST Arabidopsis thaliana protein match is: nuclear RNA polymerase D1B (TAIR:AT2G40030.1); Has 18758 Blast hits to 17462 proteins in 6889 species: Archae - 580; Bacteria - 5923; Metazoa - 1639; Fungi - 1387; Plants - 5197; Viruses - 287; Other Eukaryotes - 3745 (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_003070.9 Reference assembly

      Range
      23354685..23362589 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001334061.1 → NP_001320709.1  nuclear RNA polymerase D1A [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178WGI4, A0A1P8ANM9, A0A654EQM9

    2. NM_001334062.1 → NP_001320708.1  nuclear RNA polymerase D1A [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8ANM7, A0A654EQM9

    3. NM_001198369.1 → NP_001185298.1  nuclear RNA polymerase D1A [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001185298.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9LQ02
      UniProtKB/TrEMBL
      A0A178WGI4, A0A654EQM9
      Conserved Domains (3) summary
      cd02737
      Location:874 → 1266
      RNAP_IV_NRPD1_C; Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain
      cd10506
      Location:23 → 851
      RNAP_IV_RPD1_N; Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain
      pfam11523
      Location:1349 → 1419
      DUF3223; Protein of unknown function (DUF3223)

    4. NM_001334063.1 → NP_001320710.1  nuclear RNA polymerase D1A [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A1P8ANM8

    5. NM_104980.4 → NP_176490.2  nuclear RNA polymerase D1A [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_176490.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9LQ02
      UniProtKB/TrEMBL
      A0A178WGI4, A0A654EQM9
      Conserved Domains (3) summary
      cd02737
      Location:874 → 1266
      RNAP_IV_NRPD1_C; Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain
      cd10506
      Location:23 → 851
      RNAP_IV_RPD1_N; Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain
      pfam11523
      Location:1349 → 1419
      DUF3223; Protein of unknown function (DUF3223)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9LQ02.1

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