Home LiteratureArticle Details
PMID: 16131612 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis.

Genes & development ·Vol. 19 ·No. 18 ·2005-09-15 ·Pages 2164-75

Yoshikawa M, Peragine A, Park MY, Poethig RS

Abstract

The Arabidopsis genes, TAS2 and TAS1a, produce structurally similar noncoding transcripts that are transformed into short (21-nucleotide [nt]) and long (24-nt) siRNAs by RNA silencing pathways. Some of these short siRNAs direct the cleavage of protein-coding transcripts, and thus function as trans-acting siRNAs (ta-siRNAs). Using genetic analysis, we defined the pathway by which ta-siRNAs and other short siRNAs are generated from these loci. This process is initiated by the miR173-directed cleavage of a primary poly(A) transcript. The 3' fragment is then transformed into short siRNAs by the sequential activity of SGS3, RDR6, and DCL4: SGS3 stabilizes the fragment, RDR6 produces a complementary strand, and DCL4 cleaves the resulting double-stranded molecule into short siRNAs, starting at the end with the miR173 cleavage site and proceeding in 21-nt increments from this point. The 5' cleavage fragment is also processed by this pathway, but less efficiently. The DCL3-dependent pathway that generates long siRNAs does not require miRNA-directed cleavage and plays a minor role in the silencing of these loci. Our results define the core components of a post-transcriptional gene silencing pathway in Arabidopsis and reveal some of the features that direct transcripts to this pathway.

MeSH Terms
Arabidopsis/genetics,growth & development,metabolism Arabidopsis Proteins/chemistry,genetics,metabolism Base Sequence Gene Expression Regulation, Plant Gene Targeting Genes, Plant MicroRNAs/metabolism Models, Biological Molecular Sequence Data Mutation Protein Structure, Tertiary RNA Interference RNA Processing, Post-Transcriptional RNA, Small Interfering/biosynthesis Reverse Transcriptase Polymerase Chain Reaction Transcription, Genetic
Chemicals
Arabidopsis Proteins MicroRNAs RNA, Small Interfering
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Yoshikawa Manabu
Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6018, USA.
Peragine Angela
Park Mee Yeon
Poethig R Scott
References (68)
68 references, click to expand
  1. The small RNA profile during Drosophila melanogaster development.
    Dev Cell. 2003 Aug;5(2):337-50 PMID: 12919683
  2. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.
    Plant Cell. 2004 Aug;16(8):2089-103 PMID: 15269332
  3. Nuclear processing and export of microRNAs in Arabidopsis.
    Proc Natl Acad Sci U S A. 2005 Mar 8;102(10):3691-6 PMID: 15738428
  4. Methylation as a crucial step in plant microRNA biogenesis.
    Science. 2005 Feb 11;307(5711):932-5 PMID: 15705854
  5. 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
  6. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA.
    Science. 2002 Sep 20;297(5589):2053-6 PMID: 12242443
  7. 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
  8. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis.
    Genes Dev. 2004 Oct 1;18(19):2368-79 PMID: 15466488
  9. Transitivity-dependent and -independent cell-to-cell movement of RNA silencing.
    EMBO J. 2003 Sep 1;22(17):4523-33 PMID: 12941703
  10. RNAi-dependent and RNAi-independent mechanisms contribute to the silencing of RIPed sequences in Neurospora crassa.
    Nucleic Acids Res. 2004;32(14):4237-43 PMID: 15302921
  11. RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24-26-nucleotide RNAs.
    RNA. 2001 Nov;7(11):1522-30 PMID: 11720282
  12. Potato virus X amplicons in arabidopsis mediate genetic and epigenetic gene silencing.
    Plant Cell. 2000 Mar;12(3):369-79 PMID: 10715323
  13. Endogenous and silencing-associated small RNAs in plants.
    Plant Cell. 2002 Jul;14(7):1605-19 PMID: 12119378
  14. A biochemical framework for RNA silencing in plants.
    Genes Dev. 2003 Jan 1;17(1):49-63 PMID: 12514099
  15. ASRP: the Arabidopsis Small RNA Project Database.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D637-40 PMID: 15608278
  16. Uncoupling of RNAi from active translation in mammalian cells.
    RNA. 2005 Jan;11(1):38-44 PMID: 15574516
  17. The functions of animal microRNAs.
    Nature. 2004 Sep 16;431(7006):350-5 PMID: 15372042
  18. MicroRNAs in plants.
    Genes Dev. 2002 Jul 1;16(13):1616-26 PMID: 12101121
  19. Perspective: machines for RNAi.
    Genes Dev. 2005 Mar 1;19(5):517-29 PMID: 15741316
  20. Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics.
    Nat Rev Mol Cell Biol. 2004 Feb;5(2):89-99 PMID: 15040442
  21. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans.
    Nature. 2000 Feb 24;403(6772):901-6 PMID: 10706289
  22. MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome.
    Dev Cell. 2004 Nov;7(5):653-62 PMID: 15525527
  23. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana.
    Nat Genet. 2004 Dec;36(12):1282-90 PMID: 15565108
  24. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction.
    Dev Cell. 2003 Feb;4(2):205-17 PMID: 12586064
  25. Posttranscriptional gene silencing is not compromised in the Arabidopsis CARPEL FACTORY (DICER-LIKE1) mutant, a homolog of Dicer-1 from Drosophila.
    Curr Biol. 2003 Feb 4;13(3):236-40 PMID: 12573220
  26. A branched pathway for transgene-induced RNA silencing in plants.
    Curr Biol. 2002 Apr 16;12(8):684-8 PMID: 11967158
  27. Genetic and functional diversification of small RNA pathways in plants.
    PLoS Biol. 2004 May;2(5):E104 PMID: 15024409
  28. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14.
    Cell. 1993 Dec 3;75(5):843-54 PMID: 8252621
  29. Uridine addition after microRNA-directed cleavage.
    Science. 2004 Nov 5;306(5698):997 PMID: 15528436
  30. A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes.
    Proc Natl Acad Sci U S A. 2005 Jul 5;102(27):9703-8 PMID: 15980147
  31. A link between mRNA turnover and RNA interference in Arabidopsis.
    Science. 2004 Nov 5;306(5698):1046-8 PMID: 15528448
  32. 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
  33. MicroRNAs and other tiny endogenous RNAs in C. elegans.
    Curr Biol. 2003 May 13;13(10):807-18 PMID: 12747828
  34. The SGS3 protein involved in PTGS finds a family.
    BMC Bioinformatics. 2002 Aug 5;3:21 PMID: 12162795
  35. SHORT INTEGUMENTS1/SUSPENSOR1/CARPEL FACTORY, a Dicer homolog, is a maternal effect gene required for embryo development in Arabidopsis.
    Plant Physiol. 2002 Oct;130(2):808-22 PMID: 12376646
  36. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation.
    Science. 2003 Jan 31;299(5607):716-9 PMID: 12522258
  37. siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis.
    Genes Dev. 2004 Dec 1;18(23):2873-8 PMID: 15545622
  38. MicroRNAs: genomics, biogenesis, mechanism, and function.
    Cell. 2004 Jan 23;116(2):281-97 PMID: 14744438
  39. 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
  40. Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana.
    Plant Mol Biol. 2005 Jan;57(2):173-88 PMID: 15821876
  41. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing.
    Curr Biol. 2004 Feb 17;14(4):346-51 PMID: 14972688
  42. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway.
    Science. 2003 Sep 26;301(5641):1921-5 PMID: 14512631
  43. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways.
    Cell. 2004 Apr 2;117(1):69-81 PMID: 15066283
  44. 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
  45. A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila.
    Cell. 2004 Apr 2;117(1):83-94 PMID: 15066284
  46. Synthetic shRNAs as potent RNAi triggers.
    Nat Biotechnol. 2005 Feb;23(2):227-31 PMID: 15619616
  47. Two classes of short interfering RNA in RNA silencing.
    EMBO J. 2002 Sep 2;21(17):4671-9 PMID: 12198169
  48. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana.
    Curr Biol. 2002 Sep 3;12(17):1484-95 PMID: 12225663
  49. A species of small antisense RNA in posttranscriptional gene silencing in plants.
    Science. 1999 Oct 29;286(5441):950-2 PMID: 10542148
  50. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs.
    Mol Cell. 2004 Oct 8;16(1):69-79 PMID: 15469823
  51. RNA polymerase IV directs silencing of endogenous DNA.
    Science. 2005 Apr 1;308(5718):118-20 PMID: 15692015
  52. Mapping the 5' and 3' ends of Tetrahymena thermophila mRNAs using RNA ligase mediated amplification of cDNA ends (RLM-RACE).
    Nucleic Acids Res. 1993 Oct 25;21(21):4954-60 PMID: 8177745
  53. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP.
    EMBO J. 2002 Nov 1;21(21):5875-85 PMID: 12411505
  54. RNA-directed RNA polymerase from tomato leaves. II. Catalytic in vitro properties.
    J Biol Chem. 1993 Jun 5;268(16):11858-67 PMID: 7685023
  55. DICER-LIKE1: blind men and elephants in Arabidopsis development.
    Trends Plant Sci. 2002 Nov;7(11):487-91 PMID: 12417148
  56. Single processing center models for human Dicer and bacterial RNase III.
    Cell. 2004 Jul 9;118(1):57-68 PMID: 15242644
  57. microRNA-directed phasing during trans-acting siRNA biogenesis in plants.
    Cell. 2005 Apr 22;121(2):207-21 PMID: 15851028
  58. Messenger RNA deadenylylation precedes decapping in mammalian cells.
    Proc Natl Acad Sci U S A. 1997 May 27;94(11):5628-33 PMID: 9159123
  59. The developmental role of microRNA in plants.
    Curr Opin Plant Biol. 2005 Feb;8(1):38-44 PMID: 15653398
  60. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation.
    Cell. 2005 Mar 11;120(5):613-22 PMID: 15766525
  61. Geminivirus VIGS of endogenous genes requires SGS2/SDE1 and SGS3 and defines a new branch in the genetic pathway for silencing in plants.
    Plant J. 2004 Jun;38(6):1004-14 PMID: 15165191
  62. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation.
    Proc Natl Acad Sci U S A. 2004 Jan 27;101(4):1093-8 PMID: 14722360
  63. Initiation of silencing of maize MuDR/Mu transposable elements.
    Plant J. 2003 Mar;33(6):1013-25 PMID: 12631326
  64. Processing of primary microRNAs by the Microprocessor complex.
    Nature. 2004 Nov 11;432(7014):231-5 PMID: 15531879
  65. AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets.
    Mol Cell. 2004 Jul 23;15(2):173-83 PMID: 15260969
  66. A protein sensor for siRNA asymmetry.
    Science. 2004 Nov 19;306(5700):1377-80 PMID: 15550672
  67. RNA interference is mediated by 21- and 22-nucleotide RNAs.
    Genes Dev. 2001 Jan 15;15(2):188-200 PMID: 11157775
  68. Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi.
    Nature. 2003 Nov 20;426(6964):310-4 PMID: 14628056
Article Info
Journal
Genes & development
Abbr.
Genes Dev
ISSN
0890-9369
DOI
10.1101/gad.1352605
Published
2005-09-15
Epub
2005-00-30
Pages
2164-75
Language
English
Region
United States
NLM ID
8711660
PMCID
PMC1221887
Subset
IM
Grants
NIGMS NIH HHS · R01 GM051893 · United States
External Links
PubMed source DOI: 10.1101/gad.1352605 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2