PsRobot: A web-based plant small RNA meta-analysis toolbox

Nucleic Acids Research

Volumn 40, Issue W1, 2012, Pages

  Wu, Hua Jun ^a,b   Ma, Ying Ke ^a,b   Chen, Tong ^a,b   Wang, Meng ^a   Wang, Xiu Jie ^a  

^a INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PLANT RNA; RNA PRECURSOR; SMALL INTERFERING RNA;

ALGORITHM; ARTICLE; BIOGENESIS; COMPUTER ANALYSIS; COMPUTER PROGRAM; GENE EXPRESSION; GENE MUTATION; GENE TARGETING; NONHUMAN; PRIORITY JOURNAL; PROTEIN RNA BINDING; RELIABILITY; RNA ANALYSIS; RNA CLEAVAGE; RNA STRUCTURE; RNA TRANSCRIPTION; SMITH WATERMAN ALGORITHM;

ALGORITHMS; INTERNET; MICRORNAS; RNA PRECURSORS; RNA, MESSENGER; RNA, PLANT; RNA, SMALL UNTRANSLATED; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84864491712     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks554     Document Type: Article

References (47)

1. Jones-Rhoades, M.W., Bartel, D.P. and Bartel, B. (2006) MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant. Biol., 57, 19-53.
2. Vazquez, F., Vaucheret, H., Rajagopalan, R., Lepers, C., Gasciolli, V., Mallory, A.C., Hilbert, J.L., Bartel, D.P. and Crete, P. (2004) Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell., 16, 69-79.
3. Borsani, O., Zhu, J., Verslues, P.E., Sunkar, R. and Zhu, J.K. (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell, 123, 1279-1291.
4. Wang, X.J., Gaasterland, T. and Chua, N.H. (2005) Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome biology, 6, R30.
5. Zhang, Y., Liu, X.S., Liu, Q.R. and Wei, L. (2006) Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res., 34, 3465-3475.
6. Wang, H., Chua, N.H. and Wang, X.J. (2006) Prediction of trans-antisense transcripts in Arabidopsis thaliana. Genome Biol., 7, R92.
7. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B. and Bartel, D.P. (2002) MicroRNAs in plants. Genes Dev., 16, 1616-1626.
8. Mallory, A.C. and Vaucheret, H. (2006) Functions of microRNAs and related small RNAs in plants. Nat. Genet., 38 Suppl, S31-S36.
9. Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B. and Bartel, D.P. (2002) Prediction of plant microRNA targets. Cell, 110, 513-520.
10. Meyers, B.C., Simon, S.A. and Zhai, J. (2010) MicroRNA processing: battle of the bulge. Curr. Biol.: CB, 20, R68-R70.
11. Zilberman, D., Cao, X., Johansen, L.K., Xie, Z., Carrington, J.C. and Jacobsen, S.E. (2004) Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr. Biol., 14, 1214-1220.
12. Dunoyer, P., Brosnan, C.A., Schott, G., Wang, Y., Jay, F., Alioua, A., Himber, C. and Voinnet, O. (2010) An endogenous, systemic RNAi pathway in plants. EMBO J., 29, 1699-1712.
13. Meyers, B.C., Axtell, M.J., Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J. et al. (2008) Criteria for annotation of plant MicroRNAs. Plant Cell, 20, 3186-3190.
14. Jones-Rhoades, M.W. and Bartel, D.P. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell, 14, 787-799.
15. Dai, X., Zhuang, Z. and Zhao, P.X. (2010) Computational analysis of miRNA targets in plants: current status and challenges. Brief. Bioinform., 12, 115-121.
16. Allen, E., Xie, Z., Gustafson, A.M. and Carrington, J.C. (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 121, 207-221.
17. Fahlgren, N., Howell, M.D., Kasschau, K.D., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A., Law, T.F., Grant, S.R., Dangl, J.L. et al. (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PloS one, 2, e219.
18. Dai, X. and Zhao, P.X. (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res., 39, W155-W159.
19. Addo-Quaye, C., Miller, W. and Axtell, M.J. (2009) CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics, 25, 130-131.
20. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
21. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
22. Wang, X.J., Reyes, J.L., Chua, N.H. and Gaasterland, T. (2004) Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol, 5, R65.
23. Sunkar, R. and Zhu, J.K. (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 16, 2001-2019.
24. Lamesch, P., Berardini, T.Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Muller, R., Dreher, K., Alexander, D.L., Garcia-Hernandez, M. et al. (2011) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res., 40, D1202-D1210.
25. Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R.L., Lee, Y., Zheng, L. et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res., 35, D883-D887.
26. Tanaka, T., Antonio, B.A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H., Wu, J., Itoh, T., Sasaki, T. et al. (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res., 36, D1028-D1033.
27. Goodstein, D.M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N. et al. (2011) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res., 40, D1178-D1186.
28. German, M.A., Pillay, M., Jeong, D.H., Hetawal, A., Luo, S., Janardhanan, P., Kannan, V., Rymarquis, L.A., Nobuta, K., German, R. et al. (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol, 26, 941-946.
29. Fahlgren, N., Sullivan, C.M., Kasschau, K.D., Chapman, E.J., Cumbie, J.S., Montgomery, T.A., Gilbert, S.D., Dasenko, M., Backman, T.W., Givan, S.A. et al. (2009) Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA, 15, 992-1002.
30. Hardcastle, T.J. and Kelly, K.A. (2010) baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics, 11, 422.
31. Montgomery, T.A., Yoo, S.J., Fahlgren, N., Gilbert, S.D., Howell, M.D., Sullivan, C.M., Alexander, A., Nguyen, G., Allen, E., Ahn, J.H. et al. (2008) AGO1-miR173 complex initiates phased siRNA formation in plants. Proc. Natl. Acad. Sci. U.S.A., 105, 20055-20062.
32. Mi, S., Cai, T., Hu, Y., Chen, Y., Hodges, E., Ni, F., Wu, L., Li, S., Zhou, H., Long, C. et al. (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell, 133, 116-127.
33. Kasschau, K.D., Fahlgren, N., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A. and Carrington, J.C. (2007) Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS. Biol., 5, e57.
34. Lu, C., Kulkarni, K., Souret, F.F., MuthuValliappan, R., Tej, S.S., Poethig, R.S., Henderson, I.R., Jacobsen, S.E., Wang, W., Green, P.J. et al. (2006) MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res., 16, 1276-1288.
35. Howell, M.D., Fahlgren, N., Chapman, E.J., Cumbie, J.S., Sullivan, C.M., Givan, S.A., Kasschau, K.D. and Carrington, J.C. (2007) Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA-and tasiRNA-directed targeting. Plant Cell, 19, 926-942.
36. Wu, L., Zhou, H., Zhang, Q., Zhang, J., Ni, F., Liu, C. and Qi, Y. (2010) DNA methylation mediated by a microRNA pathway. Mol. Cell, 38, 465-475.
37. Wu, L., Zhang, Q., Zhou, H., Ni, F., Wu, X. and Qi, Y. (2009) Rice MicroRNA effector complexes and targets. Plant Cell, 21, 3421-3435.
38. Vazquez, F. (2006) Arabidopsis endogenous small RNAs: highways and byways. Trends Plant Sci., 11, 460-468.
39. Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
40. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
41. Li, L., Stoeckert, C.J. Jr and Roos, D.S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189.
42. Addo-Quaye, C., Eshoo, T.W., Bartel, D.P. and Axtell, M.J. (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr. Biol., 18, 758-762.
43. Pantaleo, V., Szittya, G., Moxon, S., Miozzi, L., Moulton, V., Dalmay, T. and Burgyan, J. (2010) Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant J, 62, 960-976.
44. Zhou M, G.L., Li P, Song X, Wei L, Chen Z, Cao X. (2010) Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica). Front. Biol., 5, 67-90.
45. Xie, Z., Allen, E., Wilken, A. and Carrington, J.C. (2005) DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A., 102, 12984-12989.
46. Willmann, M.R., Mehalick, A.J., Packer, R.L. and Jenik, P.D. (2011) MicroRNAs regulate the timing of embryo maturation in Arabidopsis. Plant Physiol., 155, 1871-1884.
47. Gustafson, A.M., Allen, E., Givan, S., Smith, D., Carrington, J.C. and Kasschau, K.D. (2005) ASRP: the Arabidopsis Small RNA Project Database. Nucleic Acids Res., 33, D637-D640.