Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis

Cell

Volumn 123, Issue 7, 2005, Pages 1279-1291

  Borsani, Omar ^a   Zhu, Jianhua ^a   Verslues, Paul E ^a   Sunkar, Ramanjulu ^a   Zhu, Jian Kang ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; COMPLEMENTARY RNA; PYRROLINE 5 CARBOXYLATE REDUCTASE; SMALL INTERFERING RNA;

ARTICLE; BIOGENESIS; EUKARYOTIC CELL; GENE FUNCTION; GENOME ANALYSIS; PLANT DEFENSE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; RNA DEGRADATION; RNA TRANSCRIPTION; SALT TOLERANCE; TRANSCRIPTION TERMINATION; TRANSLATION REGULATION;

ARABIDOPSIS; EUKARYOTA;

EID: 29244490062     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2005.11.035     Document Type: Article

References (52)

1. R. Ahlfors, S. Lang, K. Overmyer, P. Jaspers, M. Brosche, A. Taurianinen, H. Kollist, H. Tuominen, E. Belles-Boix, and M. Piippo Arabidopsis radical-induced cell death1 belongs to the WWE protein-protein interaction domain protein family and modulates abscisic acid, ethylene, and methyl jasmonate responses Plant Cell 16 2004 1925 1937
2. V. Ambros MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing Cell 113 2003 673 676
3. E. Allen, Z.X. Xie, A.M. Gustafson, G.H. Sung, J.W. Spatafora, and J.C. Carrington Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana Nat. Genet. 36 2004 1282 1290
4. E. Allen, Z.X. Xie, A.M. Gustafson, and J.C. Carrington microRNA-directed phasing during trans-acting siRNA biogenesis in plants Cell 121 2005 207 221
5. A.A. Aravin, M. Lagos-Quintana, A. Yalcin, M. Zavolan, D. Marks, B. Snyder, T. Gaasterland, J. Meyer, and T. Tuschl The small RNA profile during Drosophila melanogaster development Dev. Cell 5 2003 337 350
6. M.A. Ayliffe, J.K. Roberts, H.J. Mitchell, R. Zhang, G.J. Lawrence, J.G. Ellis, and T.J. Pryor A plant gene up-regulated at rust infection sites Plant Physiol. 129 2002 169 180
7. D.P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2004 281 297
8. D. Baulcombe RNA silencing in plants Nature 431 2004 356 363
9. P. Bertone, V. Stolc, T.E. Royce, J.S. Rozowsky, A.E. Urban, X. Zhu, J.L. Rinn, W. Tongprasit, M. Samanta, and S. Weissman Global identification of human transcribed sequences with genome tiling arrays Science 306 2004 2242 2246
10. S. Boi, G. Solda, and M.L. Tenchini Shedding light on the dark side of the genome: overlapping genes in higher eukaryotes Curr. Genomics 5 2004 509 524
11. S. Brenner, M. Johnson, J. Bridgham, G. Golda, D.H. Lloyd, D. Johnson, S.J. Luo, S. McCurdy, M. Foy, and M. Ewan Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays Nat. Biotechnol. 18 2000 630 634
12. J.C. Carrington, and V. Ambros Role of microRNAs in plant and animal development Science 301 2003 336 338
13. S.W. Chan, D. Zilberman, Z. Xie, L.K. Johansen, J.C. Carrington, and S.E. Jacobsen RNA silencing genes control de novo DNA methylation Science 303 2004 1336
14. 1-pyrroline-5- carboxylate dehydrogenase and its potential role in protection from proline toxicity Plant J. 27 2001 345 356
15. 1- pyrroline-5-carboxylate dehydrogenase in proline degradation Plant Cell 16 2004 3413 3425
16. V. Gasciolli, A.C. Mallory, D.P. Bartel, and H. Vaucheret Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs Curr. Biol. 15 2005 1494 1500
17. A.J. Hamilton, and D.C. Baulcombe A species of small antisense RNA in posttranscriptional gene silencing in plants Science 286 1999 950 952
18. A. Hamilton, O. Voinnet, L. Chappell, and D. Baulcombe Two classes of short interfering RNA in RNA silencing EMBO J. 21 2002 4671 4679
19. M.H. Han, S. Goud, L. Song, and N. Fedoroff 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
20. G.J. Hannon RNA interference Nature 418 2002 244 251
21. L. He, and G.J. Hannon MicroRNAs: small RNAs with a big role in gene regulation Nat. Rev. Genet. 5 2004 522 531
22. H. Hellmann, D. Funck, D. Rentsch, and W.B. Frommer Hypersensitivity of an Arabidopsis sugar signaling mutant toward exogenous proline application Plant Physiol. 123 2000 779 789
23. A.J. Herr, M.B. Jensen, T. Dalmay, and D.C. Baulcombe RNA polymerase IV directs silencing of endogenous DNA Science 308 2005 118 120
24. S. Iyer, and A. Caplan Products of proline catabolism can induce osmotically regulated genes in rice Plant Physiol. 116 1998 203 211
25. C.-H. Jen, I. Michalopoulos, D.R. Westhead, and P. Meyer Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation Genome Biol. 6 2005 R51
26. A. Khvorova, A. Reynolds, and S.D. Jayasena Functional siRNAs and rniRNAs exhibit strand bias Cell 115 2003 209 216
27. C. Llave, Z. Xie, K.D. Kasschau, and J.C. Carrington Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA Science 297 2002 2053 2056
28. C. Lu, S.S. Tej, S. Luo, C.D. Haudenschild, B.C. Meyers, and P.J. Green Elucidation of the small RNA component of the transcriptome Science 309 2005 1567 1569
29. G. Meister, and T. Tuschl Mechanisms of gene silencing by double-stranded RNA Nature 431 2004 343 349
30. J.B. Morel, P. Mourrain, C. Beclin, and H. Vaucheret DNA methylation and chromatin structure affect transcriptional and post-transcriptional transgene silencing in Arabidopsis Curr. Biol. 10 2000 1591 1594
31. P. Mourrain, C. Beclin, T. Elmayan, F. Feuerbach, C. Godon, J.B. Morel, D. Jouette, A.M. Lacombe, S. Nikic, and N. Picault Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance Cell 101 2000 533 542
32. M. Nomura, and H. Takagi Role of the yeast acetyltransferase Mpr1 in oxidative stress: Regulation of oxygen reactive species caused by a toxic proline catabolism intermediate Proc. Natl. Acad. Sci. USA 101 2004 12616 12621
33. Y. Onodera, J.R. Haag, T. Ream, P.C. Nunes, O. Pontes, and C.S. Pikaard Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation Cell 120 2005 613 622
34. J.F. Palatnik, E. Allen, X.L. Wu, C. Schommer, R. Schwab, J.C. Carrington, and D. Weigel Control of leaf morphogenesis by microRNAs Nature 425 2003 257 263
35. W. Park, J.J. Li, R.T. Song, J. Messing, and X.M. Chen CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana Curr. Biol. 12 2002 1484 1495
36. A. Peragine, M. Yoshikawa, G. Wu, H.L. Albrecht, and R.S. Poethig SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis Genes Dev. 18 2004 2368 2379
37. B.J. Reinhart, E.G. Weinstein, M.W. Rhoades, B. Bartel, and D.P. Bartel MicroRNAs in plants Genes Dev. 16 2002 1616 1626
38. S.E. Schauer, S.E. Jacobsen, D.W. Meinke, and A. Ray DICER-LIKE1: blind men and elephants in Arabidopsis development Trends Plant Sci. 7 2002 487 491
39. D.S. Schwarz, G. Hutvagner, T. Du, Z. Xu, N. Aronin, and P.D. Zamore Asymmetry in the assembly of the RNAi enzyme complex Cell 115 2003 199 208
40. R. Shin, and D.P. Schachtman Hydrogen peroxide mediates plant root cell response to nutrient deprivation Proc. Natl. Acad. Sci. USA 101 2004 8827 8832
41. R. Sunkar, and J.K. Zhu Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis Plant Cell 16 2004 2001 2019
42. G. Tang, B.J. Reinhart, D.P. Bartel, and P.D. Zamore A biochemical framework for RNA silencing in plants Genes Dev. 17 2003 49 63
43. F. Vazquez, V. Gasciolli, P. Crete, and H. Vaucheret 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
44. F. Vazquez, H. Vaucheret, R. Rajagopalan, C. Lepers, V. Gasciolli, A.C. Mallory, J.L. Hilbert, D.P. Bartel, and P. Crete Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs Mol. Cell 16 2004 69 79
45. T.A. Volpe, C. Kidner, I.M. Hall, G. Teng, S.I. Grewal, and R.A. Martienssen Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi Science 297 2002 1833 1837
46. X.-J. Wang, T. Gaasterland, and N.-H. Chua Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana Genome Biol. 6 2005 R30
47. Z.X. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman, S.E. Jacobsen, and J.C. Carrington Genetic and functional diversification of small RNA pathways in plants PLoS Biol. 2 2004 E104 10.1371/journal.pbio.0020104
48. Z.X. Xie, E. Allen, A. Wilken, and J.C. Carrington DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana Proc. Natl. Acad. Sci. USA 102 2005 12984 12989
49. K. Yamada, J. Lim, J.M. Dale, H.M. Chen, P. Shinn, C.J. Palm, A.M. Southwick, A.C. Wu, C. Kim, and M. Nguyen Empirical analysis of transcriptional activity in the Arabidopsis genome Science 302 2003 842 846
50. M. Yoshikawa, A. Peragine, M.Y. Park, and R.S. Poethig A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis Genes Dev. 19 2005 2164 2175
51. J.-K. Zhu Salt and drought stress signal transduction in plants Annu. Rev. Plant Biol. 53 2002 247 273
52. D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, and S.E. Jacobsen Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats Curr. Biol. 14 2004 1214 1220