Characterization and expression profiles of miRNAs in rice seeds

Nucleic Acids Research

Volumn 37, Issue 3, 2009, Pages 916-930

  Xue, Liang Jiao ^a   Zhang, Jing Jing ^a   Xue, Hong Wei ^a  

^a INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA; SMALL RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ARTICLE; CHROMOSOME; CONTROLLED STUDY; EUKARYOTE; GENE EXPRESSION; GENE FUNCTION; GENE SILENCING; HYBRIDIZATION; INTERSPERSED REPEAT; NONHUMAN; PLANT SEED; PLANT TISSUE; PRIORITY JOURNAL; RICE; RNA ANALYSIS; SEED DEVELOPMENT; TRANSPOSON; CHEMISTRY; CLASSIFICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PLANT GENOME; PRENATAL DEVELOPMENT; RETROPOSON;

EUKARYOTA;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; MICRORNAS; ORYZA SATIVA; RETROELEMENTS; RNA, UNTRANSLATED; SEEDS;

EID: 63349083143     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn998     Document Type: Article

References (81)

1. Mallory,A.C. and Vaucheret,H. (2006) Functions of microRNAs and related small RNAs in plants. Nat. Genet., 38, S31-S36.
2. Valencia-Sanchez,M.A., Liu,J., Hannon,G.J. and Parker,R. (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 20, 515-524.
3. Chapman,E.J. and Carrington,J.C. (2007) Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet., 8, 884-896.
4. 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.
5. 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.
6. Lau,N.C., Seto,A.G., Kim,J., Kuramochi-Miyagawa,S., Nakano,T., Bartel,D.P. and Kingston,R.E. (2006) Characterization of the piRNA complex from rat testes. Science, 313, 363-367.
7. Zilberman,D., Cao,X. and Jacobsen,S.E. (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science, 299, 716-719.
8. 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.
9. Xie,Z., Allen,E., Fahlgren,N., Calamar,A., Givan,S.A. and Carrington,J.C. (2005) Expression of Arabidopsis MIRNA genes. Plant Physiol., 138, 2145-2154.
10. Kurihara,Y. and Watanabe,Y. (2004) Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl Acad. Sci. USA, 101, 12753-12758.
11. 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.
12. Yu,B., Yang,Z., Li,J., Minakhina,S., Yang,M., Padgett,R.W., Steward,R. and Chen,X. (2005) Methylation as a crucial step in plant microRNA biogenesis. Science, 307, 932-935.
13. Baumberger,N. and Baulcombe,D.C. (2005) Arabidopsis ARGONAUTE1 is an RNA slicer that selectively recruits microRNAs and short interfering RNAs. Proc. Natl Acad. Sci. USA, 102, 11928-11933.
14. Lee,R.C., Feinbaum,R.L. and Ambros,V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
15. Llave,C., Kasschau,K.D., Rector,M.A. and Carrington,J.C. (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell 14, 1605-1619.
16. Reinhart,B.J., Weinstein,E.G., Rhoades,M.W., Bartel,B. and Bartel,D.P. (2002) MicroRNAs in plants. Genes Dev., 16, 1616-1626.
17. Sunkar,R. and Zhu,J.K. (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 16, 2001-2019.
18. Xie,Z., Johansen,L.K., Gustafson,A.M., Kasschau,K.D., Lellis,A.D., Zilberman,D., Jacobsen,S.E. and Carrington,J.C. (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol., 2, E104.
19. Wang,J.F., Zhou,H., Chen,Y.Q., Luo,Q.J. and Qu,L.H. (2004) Identification of 20 microRNAs from Oryza sativa. Nucleic Acids Res. 32, 1688-1695.
20. Liu,B., Li,P., Li,X., Liu,C., Cao,S., Chu,C. and Cao,X. (2005) Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice. Plant Physiol., 139, 296-305.
21. Sunkar,R., Girke,T., Jain,P.K. and Zhu,J.K. (2005) Cloning and characterization of microRNAs from rice. Plant Cell, 17, 1397-1411.
22. Lu,C., Tej,S.S., Luo,S., Haudenschild,C.D., Meyers,B.C. and Green,P.J. (2005) Elucidation of the small RNA component of the transcriptome. Science, 309, 1567-1569.
23. 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.
24. Nobuta,K., Venu,R.C., Lu,C., Beló,A., Vemaraju,K., Kulkarni,K., Wang,W., Pillay,M., Green,P.J., Wang,G. L. et al. (2007) An expression atlas of rice mRNAs and small RNAs. Nat. Biotechnol., 25, 473-477.
25. Johnson,C., Bowman,L., Adai,A.T., Vance,V. and Sundaresan,V. (2007) CSRDB: A small RNA integrated database and browser resource for cereals. Nucleic Acids Res., 35, D829-D833.
26. 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.
27. Ambros,V., Bartel,B., Bartel,D.P., Burge,C.B., Carrington,J.C., Chen,X., Dreyfuss,G., Eddy,S.R., Griffiths-Jones,S., Marshall,M. et al. (2003) A uniform system for microRNA annotation. RNA, 9, 277-279.
28. Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
29. Zhang,B.H., Pan,X.P., Wang,Q.L., Cobb,G.P. and Anderson,T.A. (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res., 15, 336-360.
30. Ruby,J.G., Jan,C., Player,C., Axtell,M.J., Lee,W., Nusbaum,C., Ge,H. and Bartel,D.P. (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell, 127, 1193-1207.
31. Duan,K., Luo,Y.H., Luo,D., Xu,Z.H. and Xue,H.W. (2005) New insights into the complex and coordinated transcriptional regulation networks underlying rice seed development through cDNA chip-based analysis. Plant Mol. Biol., 57, 785-804.
32. Thomson,J.M., Parker,J., Perou,C.M. and Hammond,S.M. (2004) A custom microarray platform for analysis of microRNA gene expression. Nat. Methods, 1, 47-53.
33. Bentwich,I., Avniel,A., Karov,Y., Aharonov,R., Gilad,S., Barad,O., Barzilai,A., Einat,P., Einav,U., Meiri,E. et al. (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet., 37, 766-770.
34. Liang,R.Q., Li,W., Li,Y., Tan,C.Y., Li,J.X., Jin,Y.X. and Ruan,K.C. (2005) An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res., 33, e17.
35. Guo,Y., Chen,Z., Zhang,L., Zhou,F., Shi,S., Feng,X., Li,B., Meng,X., Ma,X., Luo,M. et al. (2008) Distinctive microRNA profiles relating to patient survival in esophageal squamous cell carcinoma. Cancer Res., 68, 26-33.
36. Mineno,J., Okamoto,S., Ando,T., Sato,M., Chono,H., Izu,H., Takayama,M., Asada,K., Mirochnitchenko,O., Inouye,M. et al. (2006) The expression profile of microRNAs in mouse embryos. Nucleic Acids Res. 34, 1765-1771.
37. Griffiths-Jones,S., Grocock,R.J., van Dongen,S., Bateman,A. and Enright,A.J. (2006) miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 34, D140-D144.
38. 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.
39. Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
40. Schmid,M., Davison,T.S., Henz,S.R., Pape,U.J., Demar,M., Vingron,M., Schölkopf,B., Weigel,D. and Lohmann,J.U. (2005) A gene expression map of Arabidopsis thaliana development. Nat. Genet., 37, 501-506.
41. Shi,R. and Chiang,V.L. (2005) Facile means for quantifying microRNA expression by real-time PCR. Biotechniques, 39, 519-525.
42. Chen,C., Ridzon,D.A., Broomer,A.J., Zhou,Z., Lee,D.H., Nguyen,J.T., Barbisin,M., Xu,N.L., Mahuvakar,V.R., Andersen,M.R. et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res., 33, e179.
43. Caldana,C., Scheible,W.R., Mueller-Roeber,B. and Ruzicic,S. (2007) A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors. Plant Method, 3, 7.
44. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
45. Tamura,K., Dudley,J., Nei,M. and Kumar,S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24, 1596-1599.
46. Saitou,N. and Nei,M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
47. Zuckerkandl,E. and Pauling,L. (1965) Evolutionary divergence and convergence in proteins. In Bryson,V. and Vogel,H.J. (eds), Evolving Genes and Proteins. Academic Press, New York, pp. 97-166.
48. Benson,G. (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
49. Martienssen,R.A. (2003) Maintenance of heterochromatin by RNA interference of tandem repeats. Nat. Genet., 35, 213-214.
50. Wessler,S.R., Bureau,T.E. and White,S.E. (1995) LTR-retrotransposons and MITEs: Important players in the evolution of plant genomes. Curr. Opin. Genet. Dev., 5, 814-821.
51. Stark,A., Bushati,N., Jan,C.H., Kheradpour,P., Hodges,E., Brennecke,J., Bartel,D.P., Cohen,S.M. and Kellis,M. (2008) A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev., 22, 8-13.
52. Lu,S., Sun,Y.H. and Chiang,V.L. (2008) Stress-responsive microRNAs in Populus. Plant J., 55, 131-151.
53. 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.
54. Wang,J.W., Wang,L.J., Mao,Y.B., Cai,W.J., Xue,H.W. and Chen,X.Y. (2005) Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell, 17, 2204-2216.
55. Llave,C., Xie,Z., Kasschau,K.D. and Carrington,J.C. (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297, 2053-2056.
56. Yang,J.H., Han,S.J., Yoon,E.K. and Lee,W.S. (2006) Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells. Nucleic Acids Res., 34, 1892-1899.
57. Yamasaki,H., Abdel-Ghany,S.E., Cohu,C.M., Kobayashi,Y., Shikanai,T. and Pilon,M. (2007) Regulation of copper homeostasis by micro-RNA in Arabidopsis. J. Biol. Chem., 282, 16369-16378.
58. Abdel-Ghany,S.E. and Pilon,M. (2008) MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. J. Biol. Chem., 283, 15932-15945.
59. 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.
60. Schwab,R., Palatnik,J.F., Riester,M., Schommer,C., Schmid,M. and Weigel,D. (2005) Specific effects of microRNAs on the plant transcriptome. Dev. Cell, 8, 517-527.
61. Baulcombe,D. (2004) RNA silencing in plants. Nature, 431, 356-363.
62. Nikovics,K., Blein,T., Peaucelle,A., Ishida,T., Morin,H., Aida,M. and Laufs,P. (2006) The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis. Plant Cell, 18, 2929-2945.
63. Meyers,B.C., Tej,S.S., Vu,T.H., Haudenschild,C.D., Agrawal,V., Edberg,S.B., Ghazal,H. and Decola,S. (2004) The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res., 14, 1641-1653.
64. 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.
65. Nonomura,K., Morohoshi,A., Nakano,M., Eiguchi,M., Miyao,A., Hirochika,H. and Kurata,N. (2007) A germ cell specific gene of the ARGONAUTE family is essential for the progression of premeiotic mitosis and meiosis during sporogenesis in rice. Plant Cell, 19, 2583-2594.
66. Girard,A. and Hannon,G.J. (2008) Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol., 18, 136-148.
67. Yu,Z., Jian,Z., Shen,S.H., Purisima,E. and Wang,E. (2007) 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., 35, 152-164.
68. Osato,N., Yamada,H., Satoh,K., Ooka,H., Yamamoto,M., Suzuki,K., Kawai,J., Carninci,P., Ohtomo,Y., Murakami,K. et al. (2003) Antisense transcripts with rice full-length cDNAs. Genome. Biol., 5, R5.
69. Jen,C.H., Michalopoulos,I., Westhead,D.R. and Meyer,P. (2005) Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome. Biol., 6, R51.
70. Faghihi,M.A. and Wahlestedt,C. (2006) RNA interference is not involved in natural antisense mediated regulation of gene expression in mammals. Genome. Biol., 7, R38.
71. Schruff,M.C., Spielman,M., Tiwari,S., Adams,S., Fenby,N. and Scott,R.J. (2006) The AUXIN RESPONSE FACTOR 2 gene of Arabidopsis links auxin signalling, cell division, and the size of seeds and other organs. Development, 133, 251-261.
72. Matsuda,F., Miyazawa,H., Wakasa,K. and Miyagawa,H. (2005) Quantification of indole-3-acetic acid and amino acid conjugates in rice by liquid chromatography-electrospray ionization-tandem mass spectrometry. Biosci. Biotechnol. Biochem., 69, 778-783.
73. Lu,S., Sun,Y.H., Shi,R., Clark,C., Li,L. and Chiang,V.L. (2005) Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell, 17, 2186-2203.
74. Sunkar,R., Kapoor,A. and Zhu,J.K. (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell, 18, 2051-2065.
75. Pignocchi,C., Kiddle,G., Hernández,I., Foster,S.J., Asensi,A., Taybi,T., Barnes,J. and Foyer,C.H. (2006) Ascorbate oxidase-dependent changes in the redox state of the apoplast modulate gene transcript accumulation leading to modified hormone signaling and orchestration of defense processes in tobacco. Plant Physiol., 141, 423-435.
76. Potters,G., Horemans,N., Caubergs,R.J. and Asard,H. (2000) Ascorbate and dehydroascorbate influence cell cycle progression in a tobacco cell suspension. Plant Physiol., 124, 17-20.
77. Gregory,R.I., Chendrimada,T.P., Cooch,N. and Shiekhattar,R. (2005) Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell, 123, 631-640.
78. Ro,S., Park,C., Young,D., Sanders,K.M. and Yan,W. (2007) Tissue-dependent paired expression of miRNAs. Nucleic Acids Res., 35, 5944-5953.
79. 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.
80. Chapman,E.J., Prokhnevsky,A.I., Gopinath,K., Dolja,V.V. and Carrington,J.C. (2004) Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev., 18, 1179-1186.
81. Obernosterer,G., Leuschner,P.J., Alenius,M. and Martinez,J. (2006) Post-transcriptional regulation of microRNA expression. RNA, 12 1161-1167.