Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

Genome Research

Volumn 19, Issue 8, 2009, Pages 1429-1440

  Johnson, Cameron ^a   Kasprzewska, Anna ^b   Tennessen, Kristin ^a   Fernandes, John ^c   Nan, Guo Ling ^c   Walbot, Virginia ^c   Sundaresan, Venkatesan ^a   Vance, Vicki ^b   Bowman, Lewis H ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF SOUTH CAROLINA   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT RNA;

ARTICLE; INFLORESCENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT DEVELOPMENT; PLANT GENETICS; PRIORITY JOURNAL; RICE; RNA ANALYSIS;

BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; CLUSTER ANALYSIS; DATABASES, NUCLEIC ACID; FLOWERS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; MICRORNAS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; ORYZA SATIVA; RNA, PLANT; RNA, SMALL INTERFERING; RNA, UNTRANSLATED;

LILIOPSIDA; ZEA MAYS;

EID: 68149119262     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.089854.108     Document Type: Article

References (55)

1. Alleman M, Sidorenko L, McGinnis K, Seshadri V, Dorweiler JE, White J, Sikkink K, Chandler VL. 2006. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 442: 295-298. (Pubitemid 44114903)
2. Allen E, Xie Z, Gustafson AM, Carrington JC. 2005. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207-221. (Pubitemid 40546389)
3. Ambros V, Chen X. 2007. The regulation of genes and genomes by small RNAs. Development 134: 1635-1641. (Pubitemid 46796561)
4. Archak S, Nagaraju J. 2007. Computational prediction of rice (Oryza sativa) miRNA targets. Genomics Proteomics Bioinformatics 5: 196-206. (Pubitemid 351215119)
5. Arenas-Huertero C, Pérez B, Rabanal F, Blanco-Melo D, De la Rosa C, Estrada- Navarrete G, Sanchez F, Covarrubias AA, Reyes JL. 2009. Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress. Plant Mol Biol 70: 385-401.
6. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29. (Pubitemid 30257031)
7. Axtell MJ, Jan C, Rajagopalan R, Bartel DP. 2006. A two-hit trigger for siRNA biogenesis in plants. Cell 127: 565-577. (Pubitemid 44647429)
8. Axtell MJ, Snyder JA, Bartel DP. 2007. Common functions for diverse small RNAs of land plants. Plant Cell 19: 1750-1769.
9. Backman TW, Sullivan CM, Cumbie JS, Miller ZA, Chapman EJ, Fahlgren N, Givan SA, Carrington JC, Kasschau KD. 2008. Update of ASRP: The Arabidopsis Small RNA Project Database. Nucleic Acids Res 36: D982-D985. (Pubitemid 351149856)
10. Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
11. Bailey TL, Gribskov M. 1998. Methods and statistics for combining motif match scores. J Comput Biol 5: 211-221. (Pubitemid 28323813)
12. Bailey TL, Williams N, Misleh C, Li WW. 2006. MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34: 369-373. (Pubitemid 44529795)
13. Deleris A, Gallego-Bartolome J, Bao J, Kasschau KD, Carrington JC, Voinnet O. 2006. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313: 68-71. (Pubitemid 44051252)
14. Dorweiler JE, Carey CC, Kubo KM, Hollick JB, Kermicle JL, Chandler VL. 2000. Mediator of paramutation1 is required for establishment and maintenance of paramutation at multiple maize loci. Plant Cell 12: 2101-2118.
15. Eamens A, Wang MB, Smith NA, Waterhouse PM. 2008. RNA silencing in plants: Yesterday, today, and tomorrow. Plant Physiol 147: 456-468. (Pubitemid 352844295)
16. Farazi TA, Juranek SA, Tuschl T. 2008. The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 135: 1201-1214. (Pubitemid 351622465)
17. Fusaro AF, Matthew L, Smith NA, Curtin SJ, Dedic-Hagan J, Ellacott GA, Watson JM, Wang MB, Brosnan C, Carroll BJ, et al. 2006. RNA interference- inducing hairpin RNAs in plants act through the viral defence pathway. EMBO Rep 7: 1168-1175. (Pubitemid 44660575)
18. Girard A, Hannon GJ. 2008. Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol 18: 136-148.
19. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100. (Pubitemid 34280065)
20. Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD. 2005. ASRP: The Arabidopsis Small RNA Project Database. Nucleic Acids Res 33: D637-D640. (Pubitemid 40207952)
21. Heisel SE, Zhang Y, Allen E, Guo L, Reynolds TL, Yang X, Kovalic D, Roberts JK. 2008. Characterization of unique small RNA populations from rice grain. PLoS One 3: e2871. doi: 10.1371/journal.pone.0002871.
22. Henderson IR, Jacobsen SE. 2007. Epigenetic inheritance in plants. Nature 447: 418-424.
23. Huettel B, Kanno T, Daxinger L, Bucher E, van der Winden J, Matzke AJ, Matzke M. 2007. RNA-directed DNA methylation mediated by DRD1 and Pol IVb: A versatile pathway for transcriptional gene silencing in plants. Biochim Biophys Acta 1769: 358-374. (Pubitemid 46855948)
24. Itoh J, Nonomura K, Ikeda K, Yamaki S, Inukai Y, Yamagishi H, Kitano H, Nagato Y. 2005. Rice plant development: From zygote to spikelet. Plant Cell Physiol 46: 23-47. (Pubitemid 40307199)
25. Johnson C, Bowman L, Adai AT, Vance V, Sundaresan V. 2007. CSRDB: A small RNA integrated database and browser resource for cereals. Nucleic Acids Res 35: D829-D833. (Pubitemid 46056317)
26. Jones-Rhoades MW, Bartel DP. 2004. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14: 787-799.
27. Klattenhoff C, Theurkauf W. 2008. Biogenesis and germline functions of piRNAs. Development 135: 3-9.
28. Lin H. 2007. piRNAs in the germ line. Science 316: 397.
29. Liu B, Chen Z, Song X, Liu C, Cui X, Zhao X, Fang J, Xu W, Zhang H, Wang X, et al. 2007. Oryza sativa Dicer-like4 reveals a key role for small interfering RNA silencing in plant development. Plant Cell 19: 2705-2718. (Pubitemid 350046223)
30. Llave C, Xie Z, Kasschau KD, Carrington JC. 2002. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297: 2053-2056. (Pubitemid 35052534)
31. Lu C, Jeong DH, Kulkarni K, Pillay M, Nobuta K, German R, Thatcher SR, Maher C, Zhang L, Ware D, et al. 2008. Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci 105: 4951-4956. (Pubitemid 351753852)
32. Mallory AC, Elmayan T, Vaucheret H. 2008. MicroRNA maturation and action - the expanding roles of ARGONAUTEs. Curr Opin Plant Biol 11: 560-566.
33. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380. (Pubitemid 41613494)
34. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, et al. 2008. Criteria for annotation of plant microRNAs. Plant Cell 20: 3186-3190.
35. Mlotshwa S, Pruss GJ, Vance V. 2008. Small RNAs in viral infection and host defense. Trends Plant Sci 13: 375-382.
36. Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, Dalmay T. 2008. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res 18: 1602-1609.
37. Nobuta K, Venu RC, Lu C, Belo A, Vemaraju K, Kulkarni K, Wang W, Pillay M, Green PJ, Wang GL, et al. 2007. An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol 25: 473-477. (Pubitemid 46572851)
38. Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, Accerbi M, Arteaga-Vazquez M, Sidorenko L, Jeong DH, Yen Y, et al. 2008. Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci 105: 14958-14963.
39. Ouyang S, Buell CR. 2004. The TIGR Plant Repeat Databases: A collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res 32: D360-D363. (Pubitemid 38081677)
40. Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS. 2004. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes & Dev 18: 2368-2379. (Pubitemid 39304684)
41. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes & Dev 20: 3407-3425. (Pubitemid 44969159)
42. Ramachandran V, Chen X. 2008. Small RNA metabolism in Arabidopsis. Trends Plant Sci 13: 368-374.
43. Schauer SE, Jacobsen SE, Meinke DW, Ray A. 2002. DICER-LIKE1: Blind men and elephants in Arabidopsis development. Trends Plant Sci 7: 487-491. (Pubitemid 36725992)
44. Sunkar R, Girke T, Jain PK, Zhu JK. 2005. Cloning and characterization of microRNAs from rice. Plant Cell 17: 1397-1411.
45. Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK. 2008. Identification of novel and candidate miRNAs in rice by high through put sequencing. BMC Plant Biol 8: 25. doi: 10.1186/1471-2229-8-25.
46. Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MP, Moulton V, Dalmay T. 2008. High-through put sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 9: 593. doi: 10.1186/1471-2164-9-593.
47. Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert JL, Bartel DP, Crete P. 2004. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16: 69-79. (Pubitemid 39330153)
48. Vazquez F, Blevins T, Ailhas J, Boller T, Meins F Jr. 2008. Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res 36: 6429-6438.
49. Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW. 2009. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21: 1053-1069.
50. Woodhouse MR, Freeling M, Lisch D. 2006. Initiation, establishment, and maintenance of heritable MuDR transposon silencing in maize are mediated by distinct factors. PLoS Biol 4: e339. doi: 10.1371/journal.pbio.0040339. (Pubitemid 44610089)
51. Yoshikawa M, Peragine A, Park MY, Poethig RS. 2005. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes & Dev 19: 2164-2175. (Pubitemid 41330318)
52. Zhou X, Sunkar R, Jin H, Zhu JK, Zhang W. 2009. Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. Genome Res 19: 70-78.
53. Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C. 2008. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res 18: 1456-1465.
54. Zuker M. 2003a. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415. (Pubitemid 37442169)
55. Zuker, M. 2003b. Predicting nucleic acid hybridization and melting profiles. Genome inform 14: 266-268.