NRPD2A nuclear RNA polymerase D2A [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: NRPD2A
Official Full Name: nuclear RNA polymerase D2A
Primary source: TAIR:AT3G23780
Locus tag: AT3G23780
See related: Araport:AT3G23780
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: DEFECTIVE IN MERISTEM SILENCING 2; DMS2; DRD2; NRPD2; NRPE2; nuclear RNA polymerase D2A; OCP1; OVEREXPRESSOR OF CATIONIC PEROXIDASE 1
Summary: This gene encodes the second largest, catalytic subunit of the nuclear DNA-dependent RNA polymerase IV (aka RNA polymerase D). The NRPD2 protein is found at nuclear foci that overlap or are adjacent to chromocentromeres but are not fully coincident with chromocentromeres. The loss of NRPD2 leads to the loss of cytosine methylation at pericentromeric 5S genes and AtSN1 retroelements but has no discernible effect on centromere repeat methylation. This suggests that Pol IV primarily affects facultative heterochromatin rather than constitutive heterochromatin.
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Genomic context

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See NRPD2A in Genome Data Viewer

Location:: chromosome: 3

Exon count:: 8

Sequence:: Chromosome: 3; NC_003074.8 (8567572..8574209, complement)

Chromosome 3 - NC_003074.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003074.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RDR2 converts Pol IV transcripts into double-stranded RNAs and then typically adds an extra untemplated 3' terminal nucleotide to the second strands. The dicer endonuclease DCL3 cuts resulting duplexes to generate 24- and 23-nt siRNAs.
Title: Reaction Mechanisms of Pol IV, RDR2, and DCL3 Drive RNA Channeling in the siRNA-Directed DNA Methylation Pathway.
DRD1-Pol V-dependent de novo methylation may play a role in restraining the inappropriate silencing of active protein-coding genes in plants. [NRPD2]
Title: DRD1-Pol V-dependent self-silencing of an exogenous silencer restricts the non-cell autonomous silencing of an endogenous target gene.
Data demonstrate that Pol V functions independently of Pol IV, RDR2, and DCL3-mediated siRNA production to affect interphase heterochromatin organization, possibly by involving RNAs that recruit structural or chromatin-modifying proteins.
Title: RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independently of the 24-nt siRNA-directed DNA methylation pathway.
RNA Pol IV helps produce siRNAs that target de novo cytosine methylation events required for facultative heterochromatin formation and higher-order heterochromatin associations.
Title: Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation.
Results show that RNA polymerase IV (Pol IV, subunits NRPD1a and NRPD2) silences certain transposons and repetitive DNA in a short interfering RNA pathway involving RNA-dependent RNA polymerase 2 and Dicer-like 3(DCL3) [NRPD2]
Title: RNA polymerase IV directs silencing of endogenous DNA.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_001203028.2

Supported by ESTs:

NM_113282.3

Supported by ESTs:

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	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribonucleoside binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within defense response to fungus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heterochromatin formation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of immune response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulatory ncRNA-mediated gene silencing	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulatory ncRNA-mediated post-transcriptional 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

Component	Evidence Code	Pubs
part_of RNA polymerase IV complex	IDA Inferred from Direct Assay more info	PubMed
part_of RNA polymerase V complex	IDA Inferred from Direct Assay more info	PubMed
part_of RNA polymerase complex	IDA Inferred from Direct Assay more info	PubMed
located_in heterochromatin	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 D2A

NP_001189957.1

nuclear RNA polymerase D2A (NRPD2A); CONTAINS InterPro DOMAIN/s: DNA-directed RNA polymerase, subunit 2, domain 6 (InterPro:IPR007120), RNA polymerase Rpb2, domain 7 (InterPro:IPR007641), RNA polymerase, beta subunit, protrusion (InterPro:IPR007644), RNA polymerase Rpb2, domain 3 (InterPro:IPR007645), DNA-directed RNA polymerase, subunit 2 (InterPro:IPR015712), RNA polymerase Rpb2, domain 2 (InterPro:IPR007642), RNA polymerase Rpb2, domain 4 (InterPro:IPR007646), RNA polymerase, beta subunit, conserved site (InterPro:IPR007121), RNA polymerase Rpb2, domain 5 (InterPro:IPR007647); BEST Arabidopsis thaliana protein match is: nuclear RNA polymerase D2B (TAIR:AT3G18090.1).

NP_189020.2

nuclear RNA polymerase D2A (NRPD2A); CONTAINS InterPro DOMAIN/s: DNA-directed RNA polymerase, subunit 2, domain 6 (InterPro:IPR007120), RNA polymerase Rpb2, domain 7 (InterPro:IPR007641), RNA polymerase, beta subunit, protrusion (InterPro:IPR007644), RNA polymerase Rpb2, domain 3 (InterPro:IPR007645), DNA-directed RNA polymerase, subunit 2 (InterPro:IPR015712), RNA polymerase Rpb2, domain 2 (InterPro:IPR007642), RNA polymerase Rpb2, domain 4 (InterPro:IPR007646), RNA polymerase, beta subunit, conserved site (InterPro:IPR007121), RNA polymerase Rpb2, domain 5 (InterPro:IPR007647); BEST Arabidopsis thaliana protein match is: nuclear RNA polymerase D2B (TAIR:AT3G18090.1); Has 34269 Blast hits to 26505 proteins in 8656 species: Archae - 497; Bacteria - 15697; Metazoa - 591; Fungi - 7176; Plants - 2585; Viruses - 232; Other Eukaryotes - 7491 (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

NC_003074.8 Reference assembly

Range

8567572..8574209 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001203028.2 → NP_001189957.1 nuclear RNA polymerase D2A [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001189957.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q67ZK6, Q9LK40

UniProtKB/TrEMBL

A0A178VA17, A0A654FB18

Conserved Domains (2) summary

cd00653
Location:48 → 1168

RNA_pol_B_RPB2; RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase ...

pfam04566
Location:574 → 635

RNA_pol_Rpb2_4; RNA polymerase Rpb2, domain 4
NM_113282.3 → NP_189020.2 nuclear RNA polymerase D2A [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_189020.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q67ZK6, Q9LK40

UniProtKB/TrEMBL

A0A178VA17, A0A654FB18

Conserved Domains (2) summary

cd00653
Location:48 → 1168

RNA_pol_B_RPB2; RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase ...

pfam04566
Location:574 → 635

RNA_pol_Rpb2_4; RNA polymerase Rpb2, domain 4