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PMID: 12198169 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Two classes of short interfering RNA in RNA silencing.

The EMBO journal ·Vol. 21 ·No. 17 ·2002-09-02 ·Pages 4671-9

Hamilton A, Voinnet O, Chappell L, Baulcombe D

Abstract

RNA silencing is a eukaryotic genome defence system that involves processing of double-stranded RNA (dsRNA) into 21-26 nt, short interfering RNA (siRNA). The siRNA mediates suppression of genes corresponding to the dsRNA through targeted RNA degradation. In some plant systems there are additional silencing processes, involving systemic spread of silencing and RNA-directed methylation/transcriptional suppression of homologous genomic DNA. We show here that siRNAs produced in plants from a green fluorescent protein (GFP) transgene are in short (21-22 nt) and long (24-26 nt) size classes, whereas those from endogenous retroelements are only in the long class. Viral suppressors of RNA silencing and mutations in Arabidopsis indicate that these classes of siRNA have different roles. The long siRNA is dispensable for sequence-specific mRNA degradation, but correlates with systemic silencing and methylation of homologous DNA. Conversely, the short siRNA class correlates with mRNA degradation but not with systemic signalling or methylation. These findings reveal an unexpected level of complexity in the RNA silencing pathway in plants that may also apply in animals.

MeSH Terms
Adaptation, Physiological Agrobacterium tumefaciens/genetics Arabidopsis/genetics Caulimovirus/genetics Gene Silencing Genes, Reporter Genes, Viral Green Fluorescent Proteins Luminescent Proteins/biosynthesis Plant Leaves/metabolism Plants, Genetically Modified Promoter Regions, Genetic RNA, Double-Stranded/genetics RNA, Plant/classification,physiology RNA, Small Interfering RNA, Untranslated/classification,physiology RNA, Viral/genetics Recombinant Fusion Proteins/biosynthesis Retroelements/genetics Tobacco/genetics Transgenes
Chemicals
Luminescent Proteins RNA, Double-Stranded RNA, Plant RNA, Small Interfering RNA, Untranslated RNA, Viral Recombinant Fusion Proteins Retroelements Green Fluorescent Proteins
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Hamilton Andrew
The Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
Voinnet Olivier
Chappell Louise
Baulcombe David
References (62)
62 references, click to expand
  1. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics.
    Nature. 1989 Jan 26;337(6205):376-80 PMID: 2536143
  2. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA.
    Science. 2001 Aug 3;293(5531):834-8 PMID: 11452083
  3. Resistance of RNA-mediated TGS to HC-Pro, a viral suppressor of PTGS, suggests alternative pathways for dsRNA processing.
    Curr Biol. 2001 Jul 24;11(14):1119-23 PMID: 11509235
  4. Suppression of Virus Accumulation in Transgenic Plants Exhibiting Silencing of Nuclear Genes.
    Plant Cell. 1996 Feb;8(2):179-188 PMID: 12239381
  5. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.
    Nature. 1998 Feb 19;391(6669):806-11 PMID: 9486653
  6. Transcriptional silencing and promoter methylation triggered by double-stranded RNA.
    EMBO J. 2000 Oct 2;19(19):5194-201 PMID: 11013221
  7. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans.
    Genes Dev. 2001 Oct 15;15(20):2654-9 PMID: 11641272
  8. Identification, subcellular localization and some properties of a cysteine-rich suppressor of gene silencing encoded by peanut clump virus.
    Plant J. 2002 Mar;29(5):555-67 PMID: 11874569
  9. Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase.
    Plant Cell. 2002 Apr;14(4):857-67 PMID: 11971140
  10. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells.
    Nature. 2000 Mar 16;404(6775):293-6 PMID: 10749213
  11. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing.
    Cell. 2001 Jul 13;106(1):23-34 PMID: 11461699
  12. DNA methylation and chromatin structure affect transcriptional and post-transcriptional transgene silencing in Arabidopsis.
    Curr Biol. 2000 Dec 14-28;10(24):1591-4 PMID: 11137011
  13. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis.
    Nature. 2001 May 10;411(6834):212-4 PMID: 11346800
  14. A counterdefensive strategy of plant viruses: suppression of posttranscriptional gene silencing.
    Cell. 1998 Nov 13;95(4):461-70 PMID: 9827799
  15. The rde-1 gene, RNA interference, and transposon silencing in C. elegans.
    Cell. 1999 Oct 15;99(2):123-32 PMID: 10535731
  16. A calmodulin-related protein that suppresses posttranscriptional gene silencing in plants.
    Science. 2000 Oct 6;290(5489):142-4 PMID: 11021800
  17. Transgene and transposon silencing in Chlamydomonas reinhardtii by a DEAH-box RNA helicase.
    Science. 2000 Nov 10;290(5494):1159-62 PMID: 11073454
  18. Argonaute2, a link between genetic and biochemical analyses of RNAi.
    Science. 2001 Aug 10;293(5532):1146-50 PMID: 11498593
  19. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals.
    Cell. 2000 Mar 31;101(1):25-33 PMID: 10778853
  20. Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1.
    Science. 2002 Mar 29;295(5564):2456-9 PMID: 11834782
  21. A viral movement protein prevents spread of the gene silencing signal in Nicotiana benthamiana.
    Cell. 2000 Sep 29;103(1):157-67 PMID: 11051555
  22. Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans.
    Plant Cell. 1990 Apr;2(4):279-289 PMID: 12354959
  23. Post-transcriptional gene silencing by double-stranded RNA.
    Nat Rev Genet. 2001 Feb;2(2):110-9 PMID: 11253050
  24. ATP requirements and small interfering RNA structure in the RNA interference pathway.
    Cell. 2001 Nov 2;107(3):309-21 PMID: 11701122
  25. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD.
    Cell. 1999 Oct 15;99(2):133-41 PMID: 10535732
  26. A viral suppressor of gene silencing in plants.
    Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):13079-84 PMID: 9789044
  27. Agrobacterium transient expression system as a tool for the isolation of disease resistance genes: application to the Rx2 locus in potato.
    Plant J. 2000 Jan;21(1):73-81 PMID: 10652152
  28. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate.
    EMBO J. 2001 Dec 3;20(23):6877-88 PMID: 11726523
  29. Virus-encoded suppressor of posttranscriptional gene silencing targets a maintenance step in the silencing pathway.
    Proc Natl Acad Sci U S A. 2000 Nov 21;97(24):13401-6 PMID: 11078509
  30. On the role of RNA amplification in dsRNA-triggered gene silencing.
    Cell. 2001 Nov 16;107(4):465-76 PMID: 11719187
  31. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline.
    Curr Biol. 2001 Jul 10;11(13):1017-27 PMID: 11470406
  32. Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs.
    Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6562-6 PMID: 8341669
  33. Molecular biology. RNA interference.
    Science. 2000 Mar 31;287(5462):2431-3 PMID: 10766620
  34. Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants.
    Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):14147-52 PMID: 10570213
  35. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance.
    Cell. 2000 May 26;101(5):533-42 PMID: 10850495
  36. Inactivation of gene expression in plants as a consequence of specific sequence duplication.
    Proc Natl Acad Sci U S A. 1994 Apr 26;91(9):3490-6 PMID: 8170935
  37. RNA silencing as a plant immune system against viruses.
    Trends Genet. 2001 Aug;17(8):449-59 PMID: 11485817
  38. The silence of the genes.
    Curr Opin Genet Dev. 2000 Oct;10(5):562-7 PMID: 10980436
  39. Transcriptional and posttranscriptional gene silencing are mechanistically related.
    Curr Biol. 2001 Mar 20;11(6):436-40 PMID: 11301254
  40. Stable transfer of intact high molecular weight DNA into plant chromosomes.
    Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9975-9 PMID: 8790442
  41. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus.
    Cell. 2000 May 26;101(5):543-53 PMID: 10850496
  42. HC-Pro suppression of transgene silencing eliminates the small RNAs but not transgene methylation or the mobile signal.
    Plant Cell. 2001 Mar;13(3):571-83 PMID: 11251097
  43. A species of small antisense RNA in posttranscriptional gene silencing in plants.
    Science. 1999 Oct 29;286(5441):950-2 PMID: 10542148
  44. A viral protein inhibits the long range signaling activity of the gene silencing signal.
    EMBO J. 2002 Feb 1;21(3):398-407 PMID: 11823432
  45. Technical Advance. Tobacco rattle virus as a vector for analysis of gene function by silencing.
    Plant J. 2001 Jan;25(2):237-45 PMID: 11169199
  46. Systemic spread of sequence-specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA.
    Cell. 1998 Oct 16;95(2):177-87 PMID: 9790525
  47. SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis.
    EMBO J. 2001 Apr 17;20(8):2069-78 PMID: 11296239
  48. Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions.
    EMBO J. 1997 Aug 1;16(15):4738-45 PMID: 9303318
  49. Systemic signalling in gene silencing.
    Nature. 1997 Oct 9;389(6651):553 PMID: 9335491
  50. Silencing on the spot. Induction and suppression of RNA silencing in the Agrobacterium-mediated transient expression system.
    Plant Physiol. 2001 Jul;126(3):930-8 PMID: 11457942
  51. Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana.
    EMBO J. 1998 Nov 16;17(22):6739-46 PMID: 9822616
  52. Arabidopsis mutants impaired in cosuppression.
    Plant Cell. 1998 Oct;10(10):1747-58 PMID: 9761800
  53. pGreen: a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation.
    Plant Mol Biol. 2000 Apr;42(6):819-32 PMID: 10890530
  54. RNA-DNA interactions and DNA methylation in post-transcriptional gene silencing.
    Plant Cell. 1999 Dec;11(12):2291-301 PMID: 10590159
  55. Initiation and maintenance of virus-induced gene silencing
    Plant Cell. 1998 Jun;10(6):937-46 PMID: 9634582
  56. Posttranscriptional silencing of reporter transgenes in tobacco correlates with DNA methylation.
    Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10502-6 PMID: 7937983
  57. Silencing of retrotransposons in arabidopsis and reactivation by the ddm1 mutation.
    Plant Cell. 2000 Mar;12(3):357-69 PMID: 10715322
  58. RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance.
    Curr Biol. 2001 May 15;11(10):747-57 PMID: 11378384
  59. Role for a bidentate ribonuclease in the initiation step of RNA interference.
    Nature. 2001 Jan 18;409(6818):363-6 PMID: 11201747
  60. Identification and structural analysis of SINE elements in the Arabidopsis thaliana genome.
    Genes Genet Syst. 2001 Jun;76(3):169-79 PMID: 11569500
  61. RNA interference is mediated by 21- and 22-nucleotide RNAs.
    Genes Dev. 2001 Jan 15;15(2):188-200 PMID: 11157775
  62. A model for RNA-mediated gene silencing in higher plants.
    Plant Mol Biol. 1998 May;37(2):349-62 PMID: 9617806
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
DOI
10.1093/emboj/cdf464
Published
2002-09-02
Pages
4671-9
Language
English
Region
England
NLM ID
8208664
PMCID
PMC125409
Subset
IM
Corrections
ErratumIn
PMID: 26291654
External Links
PubMed source DOI: 10.1093/emboj/cdf464 PMC Full Text View journal details
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