Identification of novel maize miRNAs by measuring the precision of precursor processing

BMC Plant Biology

Volumn 11, Issue , 2011, Pages

  Jiao, Yinping ^a   Song, Weibin ^a   Zhang, Mei ^a   Lai, Jinsheng ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ZEA MAYS;

MICRORNA; PLANT RNA;

ARTICLE; GENETICS; MAIZE; METHODOLOGY; PLANT GENOME; RNA PROCESSING; SEQUENCE ANALYSIS;

GENOME, PLANT; MICRORNAS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, PLANT; SEQUENCE ANALYSIS, RNA; ZEA MAYS;

EID: 80054710686     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-11-141     Document Type: Article

References (52)

1. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116(2):281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
2. Mallory AC, Vaucheret H. Functions of microRNAs and related small RNAs in plants. Nat Genet 2006, 38(Suppl):S31-S36.
3. Mallory AC, Bartel DP, Bartel B. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 2005, 17(5):1360-1375. 10.1105/tpc.105.031716, 1091760, 15829600.
4. Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang G, Zamore PD, Barton MK, Bartel DP. MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region. Embo J 2004, 23(16):3356-3364. 10.1038/sj.emboj.7600340, 514513, 15282547.
5. Aukerman MJ, Sakai H. Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 2003, 15(11):2730-2741. 10.1105/tpc.016238, 280575, 14555699.
6. Jones-Rhoades MW, Bartel DP. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 2004, 14(6):787-799. 10.1016/j.molcel.2004.05.027, 15200956.
7. Vaucheret H, Mallory AC, Bartel DP. AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1. Mol Cell 2006, 22(1):129-136. 10.1016/j.molcel.2006.03.011, 2323247, 16600876.
8. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. MicroRNA genes are transcribed by RNA polymerase II. Embo J 2004, 23(20):4051-4060. 10.1038/sj.emboj.7600385, 524334, 15372072.
9. Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC. Expression of Arabidopsis MIRNA genes. Plant Physiol 2005, 138(4):2145-2154. 10.1104/pp.105.062943, 1183402, 16040653.
10. Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X. Methylation as a crucial step in plant microRNA biogenesis. Science 2005, 307(5711):932-935. 10.1126/science.1107130, 15705854.
11. Kurihara Y, Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci USA 2004, 101(34):12753-12758. 10.1073/pnas.0403115101, 515125, 15314213.
12. 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 2004, 14(4):346-351.
13. Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig RS. Nuclear processing and export of microRNAs in Arabidopsis. Proc Natl Acad Sci USA 2005, 102(10):3691-3696. 10.1073/pnas.0405570102, 553294, 15738428.
14. Llave C, Xie Z, Kasschau KD, Carrington JC. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002, 297(5589):2053-2056. 10.1126/science.1076311, 12242443.
15. Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 2006, 57:19-53. 10.1146/annurev.arplant.57.032905.105218, 16669754.
16. Barakat A, Wall K, Leebens-Mack J, Wang YJ, Carlson JE, Depamphilis CW. Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. Plant J 2007, 51(6):991-1003. 10.1111/j.1365-313X.2007.03197.x, 17635767.
17. Xue LJ, Zhang JJ, Xue HW. Characterization and expression profiles of miRNAs in rice seeds. Nucleic Acids Res 2009, 37(3):916-930. 10.1093/nar/gkn998, 2647296, 19103661.
18. Barakat A, Wall PK, Diloreto S, Depamphilis CW, Carlson JE. Conservation and divergence of microRNAs in Populus. BMC Genomics 2007, 8:481. 10.1186/1471-2164-8-481, 2270843, 18166134.
19. Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 2008, 18(6):957-964. 10.1101/gr.074740.107, 2413163, 18469162.
20. Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res 2008, 18(9):1456-1465. 10.1101/gr.075572.107, 2527712, 18687877.
21. Moxon S, Jing R, Szittya G, Schwach F, Rusholme PR, Moulton V, Dalmay T. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res 2008, 18(10):1602-1609. 10.1101/gr.080127.108, 2556272, 18653800.
22. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006, 20(24):3407-3425. 10.1101/gad.1476406, 1698448, 17182867.
23. Heisel SE, Zhang Y, Allen E, Guo L, Reynolds TL, Yang X, Kovalic D, Roberts JK. Characterization of unique small RNA populations from rice grain. PLoS One 2008, 3(8):e2871. 10.1371/journal.pone.0002871, 2518513, 18716673.
24. Johnson C, Kasprzewska A, Tennessen K, Fernandes J, Nan GL, Walbot V, Sundaresan V, Vance V, Bowman LH. Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res 2009, 19(8):1429-1440. 10.1101/gr.089854.108, 2720183, 19584097.
25. Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, Unrau PJ. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res 2008, 18(4):571-584. 10.1101/gr.6897308, 2279245, 18323537.
26. Bonnet E, Wuyts J, Rouze P, Van de Peer Y. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci USA 2004, 101(31):11511-11516. 10.1073/pnas.0404025101, 509231, 15272084.
27. Lindow M, Jacobsen A, Nygaard S, Mang Y, Krogh A. Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants. PLoS Comput Biol 2007, 3(11):e238. 10.1371/journal.pcbi.0030238, 2098865, 18052543.
28. Chuck G, Meeley R, Irish E, Sakai H, Hake S. The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spikelet1. Nat Genet 2007, 39(12):1517-1521. 10.1038/ng.2007.20, 18026103.
29. Lauter N, Kampani A, Carlson S, Goebel M, Moose SP. microRNA172 down-regulates glossy15 to promote vegetative phase change in maize. Proc Natl Acad Sci USA 2005, 102(26):9412-9417. 10.1073/pnas.0503927102, 1166634, 15958531.
30. Juarez MT, Kui JS, Thomas J, Heller BA, Timmermans MC. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature 2004, 428(6978):84-88. 10.1038/nature02363, 14999285.
31. Griffiths-Jones S. miRBase: microRNA sequences and annotation. Curr Protoc Bioinformatics 2010, Chapter 12:12-19.
32. Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA. Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 2006, 63(2):246-254. 10.1007/s00018-005-5467-7, 16395542.
33. Christopher M, Marja T, Lincoln S, Doreen W. Identifying MicroRNAs in Plant Genomes. Proc IEEE CSB 2004, 718-723.
34. Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D. A genome-wide characterization of microRNA genes in maize. PLoS Genet 2009, 5(11):e1000716. 10.1371/journal.pgen.1000716, 2773440, 19936050.
35. Zhang B, Pan X, Anderson TA. Identification of 188 conserved maize microRNAs and their targets. Febs Lett 2006, 580(15):3753-3762. 10.1016/j.febslet.2006.05.063, 16780841.
36. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, et al. Criteria for annotation of plant MicroRNAs. Plant Cell 2008, 20(12):3186-3190. 10.1105/tpc.108.064311, 2630443, 19074682.
37. Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, Accerbi M, Arteaga-Vazquez M, Sidorenko L, Jeong DH, Yen Y, et al. Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci USA 2008, 105(39):14958-14963. 10.1073/pnas.0808066105, 2567475, 18815367.
38. Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 2009, 21(4):1053-1069. 10.1105/tpc.109.065714, 2685623, 19376930.
39. Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL. Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 2005, 17(8):2186-2203. 10.1105/tpc.105.033456, 1182482, 15994906.
40. Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 2008, 8:25. 10.1186/1471-2229-8-25, 2292181, 18312648.
41. Kasschau KD, Xie Z, Allen E, Llave C, Chapman EJ, Krizan KA, Carrington JC. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev Cell 2003, 4(2):205-217. 10.1016/S1534-5807(03)00025-X, 12586064.
42. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants. Genes Dev 2002, 16(13):1616-1626. 10.1101/gad.1004402, 186362, 12101121.
43. Orom UA, Nielsen FC, Lund AH. MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 2008, 30(4):460-471. 10.1016/j.molcel.2008.05.001, 18498749.
44. Guo WJ, Ho TH. An abscisic acid-induced protein, HVA22, inhibits gibberellin-mediated programmed cell death in cereal aleurone cells. Plant Physiol 2008, 147(4):1710-1722. 10.1104/pp.108.120238, 2492636, 18583533.
45. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220.
46. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26(10):1135-1145. 10.1038/nbt1486, 18846087.
47. Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, Axtell MJ, Zhang W, Sunkar R. Transcriptome-wide identification of microRNA targets in rice. Plant J 2010, 62(5):742-759. 10.1111/j.1365-313X.2010.04187.x, 20202174.
48. Axtell MJ, Snyder JA, Bartel DP. Common functions for diverse small RNAs of land plants. Plant Cell 2007, 19(6):1750-1769. 10.1105/tpc.107.051706, 1955733, 17601824.
49. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al. The B73 maize genome: complexity, diversity, and dynamics. Science 2009, 326(5956):1112-1115. 10.1126/science.1178534, 19965430.
50. Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
51. Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31(13):3429-3431. 10.1093/nar/gkg599, 169005, 12824340.
52. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ. Elucidation of the small RNA component of the transcriptome. Science 2005, 309(5740):1567-1569. 10.1126/science.1114112, 16141074.