Characterization of microRNAs expression during maize seed development

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Kang, Mingming ^a   Zhao, Qian ^a   Zhu, Dengyun ^a   Yu, Jingjuan ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RIBOSOME RNA; SMALL INTERFERING RNA;

ARABIDOPSIS; ARTICLE; GENE SEQUENCE; LEAF DEVELOPMENT; MAIZE; MICROARRAY ANALYSIS; NONHUMAN; PLANT DEVELOPMENT; PLANT LEAF; PLANT SEED; PROTEIN ANALYSIS; RICE; RNA SEQUENCE; SEED DEVELOPMENT;

MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT LEAVES; RNA, PLANT; RNA, UNTRANSLATED; SEEDS; ZEA MAYS;

ANIMALIA; ZEA MAYS;

EID: 84867205057     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-360     Document Type: Article

References (72)

1. Bartel D. MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell 2004, 116(2):281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
2. Park W, Li J, Song R, Messing J, Chen X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol 2002, 12(17):1484-1495. 10.1016/S0960-9822(02)01017-5, 12225663.
3. Reinhart B, Weinstein E, Rhoades M, Bartel B, Bartel D. MicroRNAs in plants. Genes & Dev 2002, 16(13):1616-1626. 10.1101/gad.1004402, 23038810.
4. Xie Z, Allen E, Fahlgren N, Calamar A, Givan S, Carrington J. Expression of Arabidopsis MIRNA genes. Plant Physiol 2005, 138(4):2145-2154. 10.1104/pp.105.062943, 1183402, 16040653.
5. Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett R, Steward R, Chen X. Methylation as a crucial step in plant microRNA biogenesis. Science 2005, 307(5711):932. 10.1126/science.1107130, 15705854.
6. Bollman K, Aukerman M, Park M, Hunter C, Berardini T, Poethig R. HASTY, the Arabidopsis ortholog of exportin 5/MSN5, regulates phase change and morphogenesis. Development 2003, 130(8):1493-1504. 10.1242/dev.00362, 12620976.
7. Park M, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig R. Nuclear processing and export of microRNAs in Arabidopsis. Proc Nat Acad Sci USA 2005, 102(10):3691. 10.1073/pnas.0405570102, 553294, 15738428.
8. Bonnet E, Van de Peer Y, Rouzé P. The small RNA world of plants. New Phytologist 2006, 171(3):451-468. 10.1111/j.1469-8137.2006.01806.x, 16866953.
9. Jones-Rhoades M, Bartel D, 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.
10. Llave C, Kasschau K, Rector M, Carrington J. Endogenous and silencing-associated small RNAs in plants. Plant Cell Online 2002, 14(7):1605-1619.
11. Carrington J, Ambros V. Role of microRNAs in plant and animal development. Science 2003, 301(5631):336. 10.1126/science.1085242, 12869753.
12. Llave C, Xie Z, Kasschau K, Carrington J. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002, 297(5589):2053. 10.1126/science.1076311, 12242443.
13. Aukerman M, Sakai H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell Online 2003, 15(11):2730-2741.
14. Gandikota M, Birkenbihl R, Höhmann S, Cardon G, Saedler H, Huijser P. The miRNA156/157 recognition element in the 3' UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J 2007, 49(4):683-693. 10.1111/j.1365-313X.2006.02983.x, 17217458.
15. Rhoades M, Reinhart B, Lim L, Burge C, Bartel B, Bartel D. Prediction of plant microRNA targets. Cell 2002, 110(4):513-520. 10.1016/S0092-8674(02)00863-2, 12202040.
16. Phillips J, Dalmay T, Bartels D. The role of small RNAs in abiotic stress. FEBS Lett 2007, 581(19):3592-3597. 10.1016/j.febslet.2007.04.007, 17451688.
17. Sunkar R, Chinnusamy V, Zhu J, Zhu J. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 2007, 12(7):301-309. 10.1016/j.tplants.2007.05.001, 17573231.
18. Nodine M, Bartel D. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes & Dev 2010, 24(23):2678-2692. 10.1101/gad.1986710, 23038810.
19. Mallory A, Bartel D, 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 Online 2005, 17(5):1360-1375.
20. Mallory A, Dugas D, Bartel D, Bartel B. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr Biol 2004, 14(12):1035-1046. 10.1016/j.cub.2004.06.022, 15202996.
21. Jofuku K, Omidyar P, Gee Z, Okamuro J. Control of seed mass and seed yield by the floral homeotic gene APETALA2. Proc National Acad Sci U S A 2005, 102(8):3117.
22. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39(Suppl 1):D152. 3013655, 21037258.
23. Zhang B, Pan X, Anderson T. Identification of 188 conserved maize microRNAs and their targets. Febs Lett 2006, 580(15):3753-3762. 10.1016/j.febslet.2006.05.063, 16780841.
24. Zhang L, Chia J, Kumari S, Stein J, Liu Z, Narechania A, Maher C, Guill K, McMullen M, Ware D. A genome-wide characterization of microRNA genes in maize. PLoS Genet 2009, 5(11):e1000716. 10.1371/journal.pgen.1000716, 2773440, 19936050.
25. Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
26. Jiao Y, Song W, Zhang M, Lai J. Identification of novel maize miRNAs by measuring the precision of precursor processing. BMC Plant Biol 2011, 11:141. 10.1186/1471-2229-11-141, 3214924, 22014170.
27. Wang L, Liu H, Li D, Chen H. Identification and characterization of maize microRNAs involved in the very early stage of seed germination. BMC Genomics 2011, 12:154. 10.1186/1471-2164-12-154, 3066126, 21414237.
28. Palatnik J, Allen E, Wu X, Schommer C, Schwab R, Carrington J, Weigel D, et al. Control of leaf morphogenesis by microRNAs. Nature 2003, 425(6955):257-263. 10.1038/nature01958, 12931144.
29. Nag A, King S, Jack T. miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. Proc Nat Acad Sci 2009, 106(52):22534. 10.1073/pnas.0908718106, 2799693, 20007771.
30. Warthmann N, Das S, Lanz C, Weigel D. Comparative analysis of the MIR319a microRNA locus in Arabidopsis and related Brassicaceae. Mol biol Evol 2008, 25(5):892-902. 10.1093/molbev/msn029, 18296705.
31. Zhu H, Hu F, Wang R, Zhou X, Sze S, Liou L, Barefoot A, Dickman M, Zhang X. Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell 2011, 145(2):242-256. 10.1016/j.cell.2011.03.024, 21496644.
32. Vaucheret H. AGO1 homeostasis involves differential production of 21-nt and 22-nt miR168 species by MIR168a and MIR168b. PLoS One 2009, 4(7):e6442. 10.1371/journal.pone.0006442, 2714465, 19649244.
33. Ding D, Zhang L, Wang H, Liu Z, Zhang Z, Zheng Y. Differential expression of miRNAs in response to salt stress in maize roots. Ann Bot 2009, 103:29-38. 2707283, 18952624.
34. Xu Z, Zhong S, Li X, Li W, Rothstein S, Zhang S, Bi Y, Xie C. Genome-Wide Identification of MicroRNAs in Response to Low Nitrate Availability in Maize Leaves and Roots. PloS one 2011, 6(11):e28009. 10.1371/journal.pone.0028009, 3223196, 22132192.
35. Kantar M, Lucas S, Budak H. miRNA expression patterns of Triticum dicoccoides in response to shock drought stress. Planta 2011, 233(3):471-484. 10.1007/s00425-010-1309-4, 21069383.
36. Xue L, Zhang J, Xue H. Characterization and expression profiles of miRNAs in rice seeds. Nucleic Acids Res 2009, 37(3):916. 10.1093/nar/gkn998, 2647296, 19103661.
37. Yu Z, Jian Z, Shen S, Purisima E, Wang E. Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos. Nucleic acids Res 2007, 35(1):152-164. 1802562, 17158157.
38. Williams L, Carles C, Osmont K, Fletcher J. A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes. Proc Nat Acad Sci U S A 2005, 102(27):9703.
39. Hsieh T, Ibarra C, Silva P, Zemach A, Eshed-Williams L, Fischer R, Zilberman D. Genome-wide demethylation of Arabidopsis endosperm. Science 2009, 324(5933):1451. 10.1126/science.1172417, 19520962.
40. Schwarz D, Hutvágner G, Du T, Xu Z, Aronin N, Zamore P. Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003, 115(2):199-208. 10.1016/S0092-8674(03)00759-1, 14567917.
41. Buhtz A, Springer F, Chappell L, Baulcombe D, Kehr J. Identification and characterization of small RNAs from the phloem of Brassica napus. Plant J 2008, 53(5):739-749. 10.1111/j.1365-313X.2007.03368.x, 18005229.
42. Rajagopalan R, Vaucheret H, Trejo J, Bartel D. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes & dev 2006, 20(24):3407. 10.1101/gad.1476406, 23038810.
43. Okamura K, Phillips M, Tyler D, Duan H, Chou Y, Lai E. The regulatory activity of microRNA*; species has substantial influence on microRNA and 3' UTR evolution. Nat Struct Mol Biol 2008, 15(4):354-363. 10.1038/nsmb.1409, 2698667, 18376413.
44. Yang J, Phillips M, Betel D, Mu P, Ventura A, Siepel A, Chen K, Lai E. Widespread regulatory activity of vertebrate microRNA* species. RNA 2011, 17(2):312-326. 10.1261/rna.2537911, 3022280, 21177881.
45. Griffiths-Jones S, Hui J, Marco A, Ronshaugen M. MicroRNA evolution by arm switching. EMBO rep 2011, 12(2):172-177. 10.1038/embor.2010.191, 3049427, 21212805.
46. Ro S, Park C, Young D, Sanders K, Yan W. Tissue-dependent paired expression of miRNAs. Nucleic Acids Res 2007, 35(17):5944-5953. 10.1093/nar/gkm641, 2034466, 17726050.
47. Devers E, Branscheid A, May P, Krajinski F. Stars and symbiosis: microRNA-and microRNA*-mediated transcript cleavage involved in arbuscular mycorrhizal symbiosis. Plant Physiol 2011, 156(4):1990-2010. 10.1104/pp.111.172627, 3149951, 21571671.
48. Zhao M, Tai H, Sun S, Zhang F, Xu Y, Li W. Cloning and Characterization of Maize miRNAs Involved in Responses to Nitrogen Deficiency. PloS one 2012, 7(1):e29669. 10.1371/journal.pone.0029669, 3250470, 22235323.
49. German M, Pillay M, Jeong D, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis L, Nobuta K, German R, et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 2008, 26(8):941-946. 10.1038/nbt1417, 18542052.
50. Jakoby M, Weisshaar B, Dröge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F. bZIP transcription factors in Arabidopsis. Trends Plant Sci 2002, 7(3):106-111. 10.1016/S1360-1385(01)02223-3, 11906833.
51. Hirsch S, Oldroyd G. GRAS-domain transcription factors that regulate plant development. Plant Signaling & Behavior 2009, 4(8):698. 10.4161/psb.4.8.9176, 23037004.
52. Schwarz S, Grande A, Bujdoso N, Saedler H, Huijser P. The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis. Plant Mol Biol 2008, 67(1):183-195. 10.1007/s11103-008-9310-z, 2295252, 18278578.
53. Wang J, Schwab R, Czech B, Mica E, Weigel D. Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell Online 2008, 20(5):1231-1243.
54. Millar A, Gubler F. The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell Online 2005, 17(3):705-721.
55. Mica E, Gianfranceschi L, Pè M. Characterization of five microRNA families in maize. J Exp Bot 2006, 57(11):2601. 10.1093/jxb/erl013, 16820394.
56. Wu M, Tian Q, Reed J. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 2006, 133(21):4211-4218. 10.1242/dev.02602, 17021043.
57. Gruber A, Lorenz R, Bernhart S, Neuböck R, Hofacker I. The vienna RNA websuite. Nucleic acids res 2008, 36(suppl 2):W70. 2447809, 18424795.
58. Zhang B, Pan X, Cox S, Cobb G, Anderson T. Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 2006, 63(2):246-254. 10.1007/s00018-005-5467-7, 16395542.
59. Krol J, Sobczak K, Wilczynska U, Drath M, Jasinska A, Kaczynska D, Krzyzosiak W. Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design. J Biol Chem 2004, 279(40):42230. 10.1074/jbc.M404931200, 15292246.
60. Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res 2005, 15:78-91. 10.1101/gr.2908205, 540280, 15632092.
61. Allen E, Xie Z, Gustafson A, Carrington J. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005, 121(2):207-221. 10.1016/j.cell.2005.04.004, 15851028.
62. Mulder N, Apweiler R, Attwood T, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, et al. New developments in the InterPro database. Nucleic Acids Res 2007, 35(suppl 1):D224-D228. 1899100, 17202162.
63. Alves-Junior L, Niemeier S, Hauenschild A, Rehmsmeier M, Merkle T. Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana. Nucleic Acids Res 2009, 37(12):4010-4021. 10.1093/nar/gkp272, 2709567, 19417064.
64. Zhang B, Pan X, Wang Q, Cobb G, Anderson T. Computational identification of microRNAs and their targets. Comput Biol Chem 2006, 30(6):395-407. 10.1016/j.compbiolchem.2006.08.006, 17123865.
65. Lau N, Lim L, Weinstein E, Bartel D. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 2001, 294(5543):858. 10.1126/science.1065062, 11679671.
66. Hackenberg M, Sturm M, Langenberger D, Falcon-Perez J, Aransay A. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic acids res 2009, 37(suppl 2):W68-W76. 2703919, 19433510.
67. Hackenberg M, Rodríguez-Ezpeleta N, Aransay A. miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res 2011, 39(suppl 2):W132-W138. 3125730, 21515631.
68. Rice P, Longden I, Bleasby A, et al. EMBOSS: the European molecular biology open software suite. Trends Genet 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
69. Chen C, Ridzon D, Broomer A, Zhou Z, Lee D, Nguyen J, Barbisin M, Xu N, Mahuvakar V, Andersen M, et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 2005, 33(20):e179-e179. 10.1093/nar/gni178, 1292995, 16314309.
70. Varkonyi-Gasic E, Wu R, Wood M, Walton E, Hellens R. Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 2007, 3:12. 10.1186/1746-4811-3-12, 2225395, 17931426.
71. Sun Y, Lu S, Shi R, Chiang V. Computational Prediction of Plant miRNA Targets. Methods Mol Biol (Clifton, NJ) 2011, 744:175.
72. Schwab R, Palatnik J, Riester M, Schommer C, Schmid M, Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev Cell 2005, 8(4):517-527. 10.1016/j.devcel.2005.01.018, 15809034.