Endogenous trans-acting siRNAs regulate the accumulation of arabidopsis mRNAs

Molecular Cell

Volumn 16, Issue 1, 2004, Pages 69-79

  Vazquez, Franck ^a,b   Vaucheret, Hervé ^b,c   Rajagopalan, Ramya ^c,d   Lepers, Christelle ^a   Gasciolli, Virginie ^b   Mallory, Allison C ^c   Hilbert, Jean Louis ^a   Bartel, David P ^c,d   Crété, Patrice ^a  

^a Lab de Chim Macromoleculaire   (France)

^b INSTITUT JEAN PIERRE BOURGIN   (France)

^c WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; SMALL INTERFERING RNA;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; DNA CLEAVAGE; GENE CONTROL; GENE EXPRESSION; GENE IDENTIFICATION; GENE REPRESSION; GENE SILENCING; GENETIC CODE; GENETIC TRANSCRIPTION; NONHUMAN;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; CELL CYCLE PROTEINS; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; MOLECULAR SEQUENCE DATA; MUTATION; RIBONUCLEASE III; RNA, MESSENGER; RNA, SMALL INTERFERING; RNA-BINDING PROTEINS; SEQUENCE ANALYSIS, DNA;

ARABIDOPSIS;

EID: 4944225347     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2004.09.028     Document Type: Article

References (61)

1. Alonso J.M., et al. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science. 301:2003;653-657
2. Ambros V., Lee R.C., Lavanway A., Williams P.T., Jewell D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13:2003;807-818
3. Aravin A.A., Naumova N.M., Tulin A.V., Vagin V.V., Rozovsky Y.M., Gvozdev V.A. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 11:2001;1017-1027
4. Aukerman M.J., Sakai H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell. 15:2003;2730-2741
5. Bartel D.P. MicroRNAs. genomics, biogenesis, mechanism, and function Cell. 116:2004;281-297
6. Bartel B., Bartel D.P. MicroRNAs. at the root of plant development? Plant Physiol. 2:2003;709-717
7. Beclin C., Boutet S., Waterhouse P., Vaucheret H. A branched pathway for transgene-induced RNA silencing in plants. Curr. Biol. 12:2002;684-688
8. Bohmert K., Camus I., Bellini C., Bouchez D., Caboche M., Benning C. AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J. 17:1998;170-180
9. Bosher J.M., Dufourcq P., Sookhareea S., Labouesse M. RNA interference can target pre-mRNA. Consequences for gene expression in a Caenorhabditis elegans operon Genetics. 153:1999;1245-1256
10. Boutet S., Vazquez F., Liu J., Beclin C., Fagard M., Gratias A., Morel J.B., Crete P., Chen X., Vaucheret H. Arabidopsis HEN1. a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance Curr. Biol. 13:2003;843-848
11. Boutla A., Delidakis C., Tabler M. Developmental defects by antisense-mediated inactivation of micro-RNAs 2 and 13 in Drosophila and the identification of putative target genes. Nucleic Acids Res. 31:2003;4973-4980
12. Brennecke J., Hipfner D.R., Stark A., Russell R.B., Cohen S.M. bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell. 113:2003;25-36
13. Carmell M.A., Xuan Z., Zhang M.Q., Hannon G.J. The Argonaute family. tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis Genes Dev. 16:2002;2733-2742
14. Carrington J.C., Ambros V. Role of microRNAs in plant and animal development. Science. 301:2003;336-338
15. Chen X. microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science. 303:2004;2022-2025
16. Chen X., Liu J., Cheng Y., Jia D. HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development. 129:2002;1085-1094
17. Dalmay T., Hamilton A., Rudd S., Angell S., Baulcombe D.C. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell. 101:2000;543-553
18. Elbashir S.M., Leneckel W., Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15:2001;188-200
19. Elmayan T., Balzergue S., Beon F., Bourdon V., Daubremet J., Guenet Y., Mourrain P., Palauqui J.C., Vernhettes S., Vialle T., et al. Arabidopsis mutants impaired in cosuppression. Plant Cell. 10:1998;1747-1758
20. Emery J.F., Floyd S.K., Alvarez J., Eshed Y., Hawker N.P., Izhaki A., Baum S.F., Bowman J.L. Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr. Biol. 13:2003;1768-1774
21. Finnegan E.J., Matzke M.A. The small RNA world. J. Cell Sci. 116:2003;4689-4693
22. Hamilton A., Voinnet O., Chappell L., Baulcombe D. Two classes of short interfering RNA in RNA silencing. EMBO J. 21:2002;4671-4679
23. Han M.H., Goud S., Song L., Fedoroff N. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl. Acad. Sci. USA. 101:2004;1093-1098
24. He L., Hannon G.J. MicroRNAs. small RNAs with a big role in gene regulation Nat. Rev. Genet. 5:2004;522-531
25. Hunter C., Sun H., Poethig R.S. The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member. Curr. Biol. 13:2003;1734-1739
26. Jacobsen S.E., Running M.P., Meyerowitz E.M. Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Development. 126:1999;5231-5243
27. Johnston R.J., Hobert O. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature. 426:2003;845-849
28. Jones-Rhoades M.W., Bartel D.P. Computational identification of plant MicroRNAs and their targets, including a stress-induced miRNA. Mol. Cell. 14:2004;787-799
29. Kasschau K.D., Xie Z., Allen E., Llave C., Chapman E.J., Krizan K.A., Carrington J.C. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev. Cell. 4:2003;205-217
30. Khvorova A., Reynolds A., Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell. 115:2003;209-216
31. Kidner C.A., Martienssen R.A. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature. 428:2004;81-84
32. Lau N.C., Lim L.P., Weinstein E.G., Bartel D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science. 294:2001;858-862
33. Lee R.C., Feinbaum R.L., Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 75:1993;843-854
34. Lim L.P., Lau N.C., Weinstein E.G., Abdelhakim A., Yekta S., Rhoades M.W., Burge C.B., Bartel D.P. The microRNAs of Caenorhabditis elegans. Genes Dev. 17:2003;991-1008
35. Llave C., Kasschau K.D., Rector M.A., Carrington J.C. Endogenous and silencing-associated small RNAs in plants. Plant Cell. 14:2002;1605-1619. a
36. Llave C., Xie Z., Kasschau K.D., Carrington J.C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science. 297:2002;2053-2056. b
37. Lu C., Fedoroff N. A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin. Plant Cell. 12:2000;2351-2366
38. Mallory A.C., Vaucheret H. MicroRNAs. something important between the genes Curr. Opin. Plant Biol. 7:2004;120-125
39. Mallory A.C., Dugas D.V., Bartel D.P., Bartel B. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr. Biol. 14:2004;1035-1046. a
40. Mallory A.C., Reinhart B.J., Jones-Rhoades M., Tang G., Zamore P.D., Barton M.K., Bartel D.P. MicroRNA control of PHABULOSA in leaf development. importance of pairing to the microRNA 5′ region EMBO J. 23:2004;3356-3364. b
41. Morel J.B., Godon C., Mourrain P., Beclin C., Boutet S., Feuerbach F., Proux F., Vaucheret H. Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell. 14:2002;629-639
42. Moss E.G., Lee R.C., Ambros V. The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell. 88:1997;637-646
43. Mourrain P., Beclin C., Elmayan T., Feuerbach F., Godon C., Morel J.B., Jouette D., Lacombe A.M., Nikic S., Picault N., et al. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell. 101:2000;533-542
44. Muangsan N., Beclin C., Vaucheret H., Robertson D. 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. 6:2004;1004-1014
45. Palatnik J.F., Allen E., Wu X., Schommer C., Schwab R., Carrington J.C., Weigel D. Control of leaf morphogenesis by microRNAs. Nature. 425:2003;257-263
46. Park W., Li J., Song R., Messing J., Chen X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12:2002;1484-1495
47. Reinhart B.J., Slack F.J., Basson M., Pasquinelli A.E., Bettinger J.C., Rougvie A.E., Horvitz H.R., Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature. 403:2000;901-906
48. Reinhart B.J., Weinstein E.G., Rhoades M.W., Bartel B., Bartel D.P. MicroRNAs in plants. Genes Dev. 16:2002;1616-1626
49. Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., Bartel D.P. Prediction of plant microRNA targets. Cell. 110:2002;513-520
50. Samson F., Brunaud V., Balzergue S., Dubreucq B., Lepiniec L., Pelletier G., Caboche M., Lecharny A. Flagdb/fst. a database of mapped flanking insertion sites (Fsts) of arabidopsis thaliana t-dna transformants Nucleic Acids Res. 30:2002;94-97
51. Schauer S.E., Jacobsen S.E., Meinke D.W., Ray A. DICER-LIKE1. blind men and elephants in Arabidopsis development Trends Plant Sci. 7:2002;487-491
52. Schwarz D.S., Hutvagner G., Du T., Xu Z., Aronin N., Zamore P.D. Asymmetry in the assembly of the RNAi enzyme complex. Cell. 2:2003;199-208
53. Sunkar, R., and Zhu, J-K. (2004). Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell online (www.plantcell.org/cgi/ doi/10.1105/tpc.104.022830).
54. Tang G., Reinhart B.J., Bartel D.P., Zamore P.D. A biochemical framework for RNA silencing in plants. Genes Dev. 17:2003;49-63
55. Vaucheret H., Vazquez F., Crete P., Bartel D.P. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev. 18:2004;1187-1197
56. Vazquez F., Gasciolli V., Crete P., Vaucheret H. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol. 14:2004;346-351
57. Wightman B., Ha I., Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell. 75:1993;855-862
58. Xie Z., Kasschau K.D., Carrington J.C. Negative feedback regulation of Dicer-like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr. Biol. 13:2003;784-789
59. Xie, Z., Johansen, L.K., Gustafson, A.M., Kasschau, K.D., Lellis, A.D., Zilberman, D., Jacobsen, S.E., and Carrington, J.C. (2004). Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2(5): e104 DOI:10.1371/journal.pbio.0020104.
60. Xu P., Vernooy S.Y., Guo M., Hay B.A. The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol. 13:2003;790-795
61. Zilberman D., Cao X., Jacobsen S.E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science. 299:2003;716-719