SeqTar: An effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants

Nucleic Acids Research

Volumn 40, Issue 4, 2012, Pages

  Zheng, Yun ^a,b   Li, Yong Fang ^c   Sunkar, Ramanjulu ^c   Zhang, Weixiong ^a,d  

^a FUDAN UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

^c OKLAHOMA STATE UNIVERSITY   (United States)

^d WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ALGORITHM; ARABIDOPSIS; ARTICLE; BASE MISPAIRING; BASE PAIRING; DEGRADOME; GENE TARGETING; GENETIC TRANSCRIPTION; HIGH THROUGHPUT SEQUENCING; NUCLEOTIDE SEQUENCE; PLANT GENOME; POLYADENYLATION; PRIORITY JOURNAL; RICE; RNA ANALYSIS; RNA CLEAVAGE; RNA SEQUENCE; SEQUENCE ALIGNMENT; STATISTICAL ANALYSIS;

ALGORITHMS; ARABIDOPSIS; BASE PAIR MISMATCH; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; ORYZA SATIVA; POLYADENYLATION; RNA, MESSENGER; RNA, PLANT; RNA, SMALL INTERFERING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

ARABIDOPSIS;

EID: 84863238628     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1092     Document Type: Article

References (45)

1. Bartel, D. P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
2. 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. (Pubitemid 35232294)
3. Voinnet, O. (2009) Origin, biogenesis, and activity of plant MicroRNAs. Cell, 136, 669-687.
4. 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. (Pubitemid 38780852)
5. 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.
6. 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. (Pubitemid 40546389)
7. Schwab, R., Palatnik, J. F., Riester, M., Schommer, C., Schmid, M. and Weigel, D. (2005) Specific effects of microRNAs on the plant transcriptome. Develop. Cell, 8, 517-527. (Pubitemid 40450741)
8. Zhang, Y. (2005) miRU: an automated plant miRNA target prediction server. Nucleic Acids Res., 33(Suppl. 2), W701-W704. (Pubitemid 44530014)
9. 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. (Pubitemid 46953238)
10. Moxon, S., Schwach, F., Dalmay, T., MacLean, D., Studholme, D. J. and Moulton, V. (2008) A toolkit for analysing large-scale plant small RNA data sets. Bioinformatics, 24, 2252-2253.
11. Jagadeeswaran, G., Zheng, Y., Li, Y.-F. F., Shukla, L. I., Matts, J., Hoyt, P., Macmil, S. L., Wiley, G. B., Roe, B. A., Zhang, W. et al. (2009) Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families. New Phytologist, 184, 85-98.
12. Bonnet, E., He, Y., Billiau, K. and Van dePeer, Y. (2010) Tapir, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics, 26, 1566-1568.
13. Xie, F. and Zhang, B. (2010) Target-align: a tool for plant microRNA target identification. Bioinformatics, 26, 3002-3003.
14. German, M. A., Pillay, M., Jeong, D.-H. 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.
15. 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. Current Biol, 18, 758-762.
16. 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.
17. Ma, Z., Coruh, C. and Axtell, M. J. (2010) Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell, 22, 1090-1103.
18. 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.
19. Li, Y.-F., Zheng, Y., Addo-Quaye, C., Zhang, L., Saini, A., Jagadeeswaran, G., Axtell, M. J., Zhang, W. and Sunkar, R. (2010) Transcriptome-wide identification of microRNA targets in rice. Plant J., 62, 742-759.
20. Zhou, M., Gu, L., Li, P., Song, X., Wei, L., Chen, Z. and Cao, X. (2010) Degradome sequencing reveals endogenous small RNA targets in rice (Oryza Sativa l. ssp. Indica). Frontiers Biol. China, 5, 67-90.
21. Addo-Quaye, C., Snyder, J. A., Park, Y. B., Li, Y.-F., Sunkar, R. and Axtell, M. J. (2009) Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. RNA, 15, 2112-2121.
22. Pantaleo, V., Szittya, G., Moxon, S., Miozzi, L., Moulton, V., Dalmay, T. and Burgyan, J. (2010) Identification of grapevinemicroRNAs and their targets using high throughput sequencing and degradome analysis. Plant J., 62, 960-976.
23. Axtell, M. J., Jan, C., Rajagopalan, R. and Bartel, D. P. (2006) A two-hit trigger for siRNA biogenesis in plants. Cell, 127, 565-577. (Pubitemid 44647429)
24. Griffiths-Jones, S., Saini, H. K., vanDongen, S. and Enright, A. J. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res., 36(Suppl. 1), D154-D158. (Pubitemid 351149713)
25. Jones-Rhoades, M. W. and Bartel, D. P. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Molecular Cell, 14, 787-799. (Pubitemid 38780852)
26. Williams, L., Carles, C. C., Osmont, K. S. and Fletcher, J. C. (2005) 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. USA, 102, 9703-9708. (Pubitemid 40981744)
27. Wu, G., Park, M. Y. Y., Conway, S. R., Wang, J.-W. W., Weigel, D. and Poethig, R. S. (2009) The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell, 138, 750-759.
28. 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. (Pubitemid 44061017)
29. Fahlgren, N., Jogdeo, S., Kasschau, K. D., Sullivan, C. M., Chapman, E. J., Laubinger, S., Smith, L. M., Dasenko, M., Givan, S. A., Weigel, D. et al. (2010) MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell, 22, 1074-1089.
30. Jiao, Y., Wang, Y., Xue, D., Wang, J., Yan, M., Liu, G., Dong, G., Zeng, D., Lu, Z., Zhu, X. et al. (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat. Genet., 42, 541-544.
31. Miura, K., Ikeda, M., Matsubara, A., Song, X.-J., Ito, M., Asano, K., Matsuoka, M., Kitano, H. and Ashikari, M. (2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat. Genet., 42, 545-549.
32. Luo, Y.-C. C., Zhou, H., Li, Y., Chen, J.-Y. Y., Yang, J.-H. H., Chen, Y.-Q. Q. and Qu, L.-H. H. (2006) Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post-embryogenic development. FEBS Lett., 580, 5111-5116. (Pubitemid 44332385)
33. Liu, Q., Zhang, Y.-C., Wang, C.-Y., Luo, Y.-C., Huang, Q.-J., Chen, S.-Y., Zhou, H., Qu, L.-H. and Chen, Y.-Q. (2009) Expression analysis of phytohormone-regulated microRNAs in rice, implying their regulation roles in plant hormone signaling. FEBS Lett., 583, 723-728.
34. Sunkar, R., Girke, T., Jain, P. K. and Zhu, J.-K. (2005) Cloning and characterization of microRNAs from rice. Plant Cell, 17, 1397-1411. (Pubitemid 43138193)
35. Lu, C., Jeong, D.-H., Kulkarni, K., Pillay, M., Nobuta, K., German, R., Thatcher, S. R., 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. USA, 105, 4951-4956. (Pubitemid 351753852)
36. Zhu, Q.-H., Spriggs, A., Matthew, L., Fan, L., Kennedy, G., Gubler, F. and Helliwell, C. (2008) A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res., 18, 1456-1465.
37. Sunkar, R., Zhou, X., Zheng, Y., Zhang, W. and Zhu, J.-K. (2008) Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol, 8, 25.
38. Lacombe, S., Nagasaki, H., Santi, C., Duval, D., Piegu, B., Bangratz, M., Breitler, J.-C., Guiderdoni, E., Brugidou, C., Hirsch, J. et al. (2008) Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice. BMC Plant Biol., 8, 123.
39. Yang, J.-H., Li, J.-H., Shao, P., Zhou, H., Chen, Y.-Q. and Qu, L.-H. (2011) starBase: a database for exploring microRNA-RNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res., 39(Suppl. 1), D202-D209.
40. English, J. J., Davenport, G. F., Elmayan, T., Vaucheret, H. and Baulcombe, D. (1997) Requirement of sense transcription for homology-dependent virus resistance and trans-inactivation. Plant J., 12, 597-603. (Pubitemid 27434038)
41. Rajagopalan, R., Vaucheret, H., Trejo, J. and Bartel, D. P. (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev., 20, 3407-3425. (Pubitemid 44969159)
42. Storey, J. D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445. (Pubitemid 37033947)
43. Mallory, A. C., Reinhart, B. J., Jones-Rhoades, M. W., Tang, G., Zamore, P. D., Barton, M. K. and Bartel, D. P. (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 50 region. EMBO J., 23, 3356-3364. (Pubitemid 39209159)
44. Poliseno, L., Salmena, L., Zhang, J., Carver, B., Haveman, W. J. and Pandolfi, P. P. (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature, 465, 1033-1038.
45. Shin, C., Nam, J.-W., Farh, K. K., Chiang, H. R., Shkumatava, A. and Bartel, D. P. (2010) Expanding the microRNA targeting code: Functional sites with centered pairing. Mol Cell, 38, 789-802.