RDR2 RNA-dependent RNA polymerase 2 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: RDR2
Official Full Name: RNA-dependent RNA polymerase 2
Primary source: TAIR:AT4G11130
Locus tag: AT4G11130
See related: Araport:AT4G11130
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: AtRDR2; RNA-dependent RNA polymerase 2; SILENCING MOVEMENT DEFICIENT 1; SMD1; T22B4.110; T22B4_110
Summary: Encodes RNA-dependent RNA polymerase that is required for endogenous siRNA (but not miRNA) formation. Nomenclature according to Xie, et al. (2004).
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Genomic context

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See RDR2 in Genome Data Viewer

Location:: chromosome: 4

Exon count:: 4

Sequence:: Chromosome: 4; NC_003075.7 (6780449..6784632)

Chromosome 4 - NC_003075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003075.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Synergistic action of the Arabidopsis spliceosome components PRP39a and SmD1b in promoting posttranscriptional transgene silencing.
Title: Synergistic action of the Arabidopsis spliceosome components PRP39a and SmD1b in promoting posttranscriptional transgene silencing.
Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA.
Title: Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA.
Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2.
Title: Structure and RNA template requirements of Arabidopsis RNA-DEPENDENT RNA POLYMERASE 2.
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.
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.
JMJ24 binds to RDR2 and is required for the basal level transcription of silenced loci in Arabidopsis.
Title: JMJ24 binds to RDR2 and is required for the basal level transcription of silenced loci in Arabidopsis.
These findings begin to reveal features of Pol IV/RDR2-mediated transcription at the heart of genome stability in plants.
Title: Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis.
Results suggest that the physical and mechanistic coupling of Pol IV and RDR2 results in the channeled synthesis of double-stranded precursors for siRNA biogenesis.
Title: In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing.
The data suggest a mechanism whereby IBM1 regulates a series of protein-coding genes including RDR2 through the RdDM-dependent control of siRNA biogenesis.
Title: IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis.
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.

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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_117183.3

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA/RNA hybrid binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA-dependent RNA polymerase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within defense response to fungus	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in response to salicylic acid	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within siRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in siRNA transcription	IDA Inferred from Direct Assay 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
located_in nucleolus	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: RNA-dependent RNA polymerase 2

NP_192851.1

RNA-dependent RNA polymerase 2 (RDR2); CONTAINS InterPro DOMAIN/s: RNA-dependent RNA polymerase, eukaryotic-type (InterPro:IPR007855); BEST Arabidopsis thaliana protein match is: RNA-dependent RNA polymerase 1 (TAIR:AT1G14790.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (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_003075.7 Reference assembly

Range

6780449..6784632

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_117183.3 → NP_192851.1 RNA-dependent RNA polymerase 2 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_192851.1

Status: REVIEWED

UniProtKB/Swiss-Prot

O82504

UniProtKB/TrEMBL

A0A654FN97

Conserved Domains (1) summary

pfam05183
Location:394 → 919

RdRP; RNA dependent RNA polymerase