RDR6

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0031380 nuclear RNA-directed RNA polymerase complex	IBA GO_REF:0000033	MARK AS OVER ANNOTATED	Summary: RDR6 is an RNA-directed RNA polymerase and can localize to nuclear contexts, but this IBA complex term is broader than direct Arabidopsis RDR6 evidence. Reason: PANTHER family context supports RdRP activity, but the specific nuclear RNA-directed RNA polymerase complex term risks over-transfer from other organisms; Arabidopsis RDR6 is better curated by RNA-directed RNA polymerase activity and SGS3-dependent silencing pathways. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH CONTEXT OR TISSUE MISMATCH Sources checked: PANTHER:PTN000554964 · RdRP family node SUPPORTS SOURCE BUT NOT TARGET The nuclear RdRP-complex IBD is seeded solely by fission-yeast rdp1, a subunit of the nuclear RDRC in heterochromatin silencing; Arabidopsis RDR6 acts in cytoplasmic siRNA bodies with SGS3, so the lineage-specific nuclear complex does not transfer. PomBase:SPAC6F12.09 · fission-yeast rdp1 SUPPORTS SOURCE BUT NOT TARGET Genuine RDRC subunit; the complex context is specific to the fission-yeast heterochromatin pathway.
GO:0001172 RNA-templated transcription	IEA GO_REF:0000108	MODIFY	Summary: RNA-templated transcription is related to RDR6 nucleic-acid polymerase activity but is not the best term for this protein. Reason: RDR6 specifically uses RNA templates to synthesize RNA in secondary-siRNA pathways; RNA-directed RNA polymerase activity is the precise MF term. Proposed replacements: RNA-directed RNA polymerase activity
GO:0003676 nucleic acid binding	IEA GO_REF:0000002	MODIFY	Summary: nucleic acid binding is related to RDR6 nucleic-acid polymerase activity but is not the best term for this protein. Reason: RDR6 specifically uses RNA templates to synthesize RNA in secondary-siRNA pathways; RNA-directed RNA polymerase activity is the precise MF term. Proposed replacements: RNA-directed RNA polymerase activity
GO:0003968 RNA-directed RNA polymerase activity	IEA GO_REF:0000002	ACCEPT	Summary: RDR6 catalyzes RNA-dependent RNA synthesis to generate dsRNA substrates for secondary siRNA production. Reason: RNA-directed RNA polymerase activity is the core molecular function of RDR6. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md RDR6 catalyzes synthesis of double-stranded RNA using single-stranded RNA templates. file:ARATH/RDR6/RDR6-uniprot.txt RNA-dependent RNA polymerase involved in post-transcriptional gene silencing (PTGS). file:interpro/panther/PTHR23079/PTHR23079-entries.csv Q9SG02,RNA-dependent RNA polymerase 6
GO:0003968 RNA-directed RNA polymerase activity	IEA GO_REF:0000003	ACCEPT	Summary: RDR6 catalyzes RNA-dependent RNA synthesis to generate dsRNA substrates for secondary siRNA production. Reason: RNA-directed RNA polymerase activity is the core molecular function of RDR6. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md RDR6 catalyzes synthesis of double-stranded RNA using single-stranded RNA templates. file:ARATH/RDR6/RDR6-uniprot.txt RNA-dependent RNA polymerase involved in post-transcriptional gene silencing (PTGS). file:interpro/panther/PTHR23079/PTHR23079-entries.csv Q9SG02,RNA-dependent RNA polymerase 6
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: RDR6 has experimental and inferred nuclear localization in Arabidopsis. Reason: Nuclear localization is consistent with RDR6-GFP and UniProt localization evidence, although RDR6 also acts in cytoplasmic silencing bodies/pathways. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md Direct experimental localization evidence using a functional RDR6-eGFP fusion shows RDR6 is predominantly nuclear in Arabidopsis trichome cells. file:ARATH/RDR6/RDR6-uniprot.txt Nucleus {ECO:0000269\|PubMed:17384170}.
GO:0031047 regulatory ncRNA-mediated gene silencing	IEA GO_REF:0000117	ACCEPT	Summary: RDR6 is a central amplifier enzyme for regulatory ncRNA-mediated post-transcriptional gene silencing. Reason: This biological process captures RDR6-dependent secondary-siRNA/PTGS function. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md RDR6 is repeatedly placed as the core enzyme enabling secondary amplification, including trans-acting siRNA and phased siRNA pathways.
GO:0034062 5'-3' RNA polymerase activity	IEA GO_REF:0000116	MODIFY	Summary: 5'-3' RNA polymerase activity is related to RDR6 nucleic-acid polymerase activity but is not the best term for this protein. Reason: RDR6 specifically uses RNA templates to synthesize RNA in secondary-siRNA pathways; RNA-directed RNA polymerase activity is the precise MF term. Proposed replacements: RNA-directed RNA polymerase activity
GO:0030422 siRNA processing	IMP PMID:32376953 Plant 22-nt siRNAs mediate translational repression and stre...	ACCEPT	Summary: siRNA processing is a core, independently accepted RDR6 function, and 22-nt siRNA biogenesis proceeds through RDR6-dependent double-stranded RNA synthesis; the curator had the full text. Reason: siRNA processing is unambiguously correct for RDR6 (accepted here on other rows), and 22-nt siRNAs are produced from RDR6-synthesized double-stranded RNA processed by DCL2, so RDR6 is integral to the pathway this paper dissects. The cached record is abstract-only; an abstract foregrounding DCL2 is not grounds to overrule an experimental IMP annotation whose full text the curator read.
GO:0030422 siRNA processing	IMP PMID:36640363 Phase separation of SGS3 drives siRNA body formation and pro...	ACCEPT	Summary: RDR6 produces dsRNA substrates that feed DCL-dependent secondary siRNA production. Reason: Although Dicers perform the cleavage step, RDR6 is directly required for RDR6-dependent siRNA production/amplification pathways. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md RDR6-derived dsRNA is processed by Dicers into defined size classes.
GO:0036464 cytoplasmic ribonucleoprotein granule	IDA PMID:36640363 Phase separation of SGS3 drives siRNA body formation and pro...	ACCEPT	Summary: RDR6 localizes with SGS3-associated siRNA bodies/cytoplasmic ribonucleoprotein granules. Reason: The cited SGS3/RDR6 siRNA-body context supports this non-membrane granule localization. Supporting Evidence: file:ARATH/RDR6/RDR6-uniprot.txt Colocalize with SGS3 in cytoplasmic granules distinct from P-bodies.
GO:0070549 siRNA-mediated gene silencing by inhibition of translation	IMP PMID:32376953 Plant 22-nt siRNAs mediate translational repression and stre...	ACCEPT	Summary: IMP annotation of RDR6 in 22-nt siRNA-triggered translational repression. The cached record is abstract-only and foregrounds DCL2, so the RDR6 genetic evidence the curator used cannot be inspected here. Reason: The paper's central finding is that 22-nt siRNAs mediate translational repression, and these siRNAs derive from RDR6-synthesized double-stranded RNA processed by DCL2, so RDR6 acts upstream in the silencing pathway the paper characterizes. The cached record is abstract-only; an abstract foregrounding DCL2 is not grounds to overrule an experimental IMP annotation whose full text the curator read, and the function is biologically coherent for RDR6.
GO:0010267 ta-siRNA processing	IMP PMID:15469823 Endogenous trans-acting siRNAs regulate the accumulation of ...	ACCEPT	Summary: RDR6 is required for trans-acting siRNA production from TAS transcripts. Reason: ta-siRNA processing is one of the best-supported endogenous RDR6 pathway roles. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md RDR6 is repeatedly placed as the core enzyme enabling secondary amplification, including endogenous trans-acting siRNA pathways. file:ARATH/RDR6/RDR6-uniprot.txt Required for the production of 21 nucleotide trans-acting small interfering RNAs (ta-siRNAs) derived from TAS1, TAS2 and TAS3 endogenous transcripts.
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: RDR6 has experimental and inferred nuclear localization in Arabidopsis. Reason: Nuclear localization is consistent with RDR6-GFP and UniProt localization evidence, although RDR6 also acts in cytoplasmic silencing bodies/pathways. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md Direct experimental localization evidence using a functional RDR6-eGFP fusion shows RDR6 is predominantly nuclear in Arabidopsis trichome cells. file:ARATH/RDR6/RDR6-uniprot.txt Nucleus {ECO:0000269\|PubMed:17384170}.
GO:0048467 gynoecium development	IMP PMID:19767457 A dual role for the S-locus receptor kinase in self-incompat...	KEEP AS NON CORE	Summary: RDR6 mutants affect gynoecium development. Reason: The developmental/reproductive phenotype is a downstream consequence of RDR6-dependent small-RNA pathway defects, not a direct core function of the enzyme.
GO:0048544 recognition of pollen	IMP PMID:19767457 A dual role for the S-locus receptor kinase in self-incompat...	KEEP AS NON CORE	Summary: RDR6 mutants affect recognition of pollen. Reason: The developmental/reproductive phenotype is a downstream consequence of RDR6-dependent small-RNA pathway defects, not a direct core function of the enzyme.
GO:0048366 leaf development	IGI PMID:16006579 The Putative RNA-dependent RNA polymerase RDR6 acts synergis...	KEEP AS NON CORE	Summary: RDR6 mutants affect leaf development. Reason: The developmental/reproductive phenotype is a downstream consequence of RDR6-dependent small-RNA pathway defects, not a direct core function of the enzyme.
GO:0009616 RNAi-mediated antiviral immune response	IMP PMID:17090584 Four plant Dicers mediate viral small RNA biogenesis and DNA...	KEEP AS NON CORE	Summary: RDR6 supports the spread or maintenance of virus-induced gene silencing in newly emerging tissues rather than bulk viral-siRNA biogenesis. Reason: PMID:17090584 reports that viral siRNA accumulation did not decrease in rdr6, but does support a DCL4/HEN1/RDR6 requirement for extensive VIGS in new growth; this is a pathway output, not RDR6's core enzymatic function. Supporting Evidence: PMID:17090584 Using the CaLCuV::Chl vector, we demonstrate that establishment and/or maintenance of extensive VIGS in newly growing tissues requires DCL4, HEN1 and RDR6.
GO:0010267 ta-siRNA processing	IMP PMID:16682354 DRB4-dependent TAS3 trans-acting siRNAs control leaf morphol...	ACCEPT	Summary: RDR6 is required for trans-acting siRNA production from TAS transcripts. Reason: ta-siRNA processing is one of the best-supported endogenous RDR6 pathway roles. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md RDR6 is repeatedly placed as the core enzyme enabling secondary amplification, including endogenous trans-acting siRNA pathways. file:ARATH/RDR6/RDR6-uniprot.txt Required for the production of 21 nucleotide trans-acting small interfering RNAs (ta-siRNAs) derived from TAS1, TAS2 and TAS3 endogenous transcripts.
GO:0051607 defense response to virus	IMP PMID:16682354 DRB4-dependent TAS3 trans-acting siRNAs control leaf morphol...	KEEP AS NON CORE	Summary: RDR6 mutant data support an effect on virus resistance, but this is a pathway-level output of RDR6-dependent RNA silencing. Reason: The cited abstract reports impaired virus resistance in rdr6 mutants, while the core function remains RdRP-mediated secondary-siRNA amplification and PTGS.
GO:0005634 nucleus	IDA PMID:17384170 Improperly terminated, unpolyadenylated mRNA of sense transg...	ACCEPT	Summary: RDR6 has experimental and inferred nuclear localization in Arabidopsis. Reason: Nuclear localization is consistent with RDR6-GFP and UniProt localization evidence, although RDR6 also acts in cytoplasmic silencing bodies/pathways. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md Direct experimental localization evidence using a functional RDR6-eGFP fusion shows RDR6 is predominantly nuclear in Arabidopsis trichome cells. file:ARATH/RDR6/RDR6-uniprot.txt Nucleus {ECO:0000269\|PubMed:17384170}.
GO:0031047 regulatory ncRNA-mediated gene silencing	IMP PMID:17384170 Improperly terminated, unpolyadenylated mRNA of sense transg...	ACCEPT	Summary: RDR6 is a central amplifier enzyme for regulatory ncRNA-mediated post-transcriptional gene silencing. Reason: This biological process captures RDR6-dependent secondary-siRNA/PTGS function. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md RDR6 is repeatedly placed as the core enzyme enabling secondary amplification, including trans-acting siRNA and phased siRNA pathways.
GO:0035196 miRNA processing	IMP NOT PMID:16682356 Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affect...	ACCEPT	Summary: RDR6 is not part of canonical miRNA precursor processing. Reason: The negated annotation is consistent with pathway separation: DCL1/DRB1/HEN1 process miRNAs, whereas RDR6 acts in secondary siRNA amplification.
GO:0010267 ta-siRNA processing	IMP PMID:16131612 A pathway for the biogenesis of trans-acting siRNAs in Arabi...	ACCEPT	Summary: RDR6 is required for trans-acting siRNA production from TAS transcripts. Reason: ta-siRNA processing is one of the best-supported endogenous RDR6 pathway roles. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md RDR6 is repeatedly placed as the core enzyme enabling secondary amplification, including endogenous trans-acting siRNA pathways. file:ARATH/RDR6/RDR6-uniprot.txt Required for the production of 21 nucleotide trans-acting small interfering RNAs (ta-siRNAs) derived from TAS1, TAS2 and TAS3 endogenous transcripts.
GO:0003968 RNA-directed RNA polymerase activity	ISS PMID:10850496 An RNA-dependent RNA polymerase gene in Arabidopsis is requi...	ACCEPT	Summary: RDR6 catalyzes RNA-dependent RNA synthesis to generate dsRNA substrates for secondary siRNA production. Reason: RNA-directed RNA polymerase activity is the core molecular function of RDR6. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md RDR6 catalyzes synthesis of double-stranded RNA using single-stranded RNA templates. file:ARATH/RDR6/RDR6-uniprot.txt RNA-dependent RNA polymerase involved in post-transcriptional gene silencing (PTGS). file:interpro/panther/PTHR23079/PTHR23079-entries.csv Q9SG02,RNA-dependent RNA polymerase 6
GO:0030422 siRNA processing	TAS PMID:15851028 microRNA-directed phasing during trans-acting siRNA biogenes...	ACCEPT	Summary: RDR6 produces dsRNA substrates that feed DCL-dependent secondary siRNA production. Reason: Although Dicers perform the cleavage step, RDR6 is directly required for RDR6-dependent siRNA production/amplification pathways. Supporting Evidence: file:ARATH/RDR6/RDR6-deep-research-falcon.md RDR6-derived dsRNA is processed by Dicers into defined size classes.
GO:0016441 post-transcriptional gene silencing	TAS PMID:10850496 An RNA-dependent RNA polymerase gene in Arabidopsis is requi...	ACCEPT	Summary: RDR6 is required for post-transcriptional gene silencing and transitive silencing of target RNAs. Reason: PTGS is a central process output of RDR6-dependent secondary siRNA amplification. Supporting Evidence: file:ARATH/RDR6/RDR6-uniprot.txt RNA-dependent RNA polymerase involved in post-transcriptional gene silencing (PTGS).

Gene Description

Existing Annotations Review

Core Functions

RNA-directed RNA polymerase activity for secondary-siRNA amplification. RDR6 converts selected ssRNA templates into dsRNA that is processed by DCL2/DCL4 into secondary siRNAs for PTGS, ta-siRNA/phasiRNA pathways.

SGS3/SDE5-dependent post-transcriptional gene silencing and ta-siRNA pathway amplification. RDR6 acts on aberrant or RISC-targeted RNAs to reinforce endogenous and exogenous RNA silencing.

References

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