MicroRNAs in the shoot apical meristem of soybean

Journal of Experimental Botany

Volumn 62, Issue 8, 2011, Pages 2495-2506

  Wong, Chui E ^a   Zhao, Ying Tao ^b,c   Wang, Xiu Jie ^b   Croft, Larry ^d   Wang, Zhong Hua ^d   Haerizadeh, Farzad ^a   Mattick, John S ^d   Singh, Mohan B ^a   Carroll, Bernard J ^d   Bhalla, Prem L ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^d UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Development; meristem; microRNAs; soybean

Indexed keywords

MESSENGER RNA; MICRORNA; PLANT RNA;

ARTICLE; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; IN SITU HYBRIDIZATION; MERISTEM; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT LEAF; SOYBEAN; ULTRASTRUCTURE;

BASE SEQUENCE; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION, PLANT; IN SITU HYBRIDIZATION; MERISTEM; MICRORNAS; MOLECULAR SEQUENCE DATA; PLANT LEAVES; RNA, MESSENGER; RNA, PLANT; SEQUENCE ANALYSIS, DNA; SOYBEANS;

GLYCINE MAX;

EID: 79957501940     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/erq437     Document Type: Article

References (64)

1. Abdel-Ghany SE, Pilon M. 2008. MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. Journal of Biological Chemistry 283, 15932-15945.
2. Achard P, Herr A, Baulcombe DC, Harberd NP. 2004. Modulation of floral development by a gibberellin-regulated microRNA. Development 131, 3357-3365. (Pubitemid 39139882)
3. Aida M, Ishida T, Fukaki H, Fujisawa H, Tasaka M. 1997. Genes involved in organ separation in Arabidopsis: An analysis of the cupshaped cotyledon mutant. The Plant Cell 9, 841-857. (Pubitemid 28173836)
4. Allen RS, Li JY, Stahle MI, Dubroue A, Gluber F, Millar AA. 2007. Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proceedings of the National Academy of Sciences, USA 104, 16371-16376. (Pubitemid 350099411)
5. Arenas-Huertero C, Pérez B, Rabanal F, Blanco-Melo D, De la Rosa C, Estrada-Navarrete G, Covarrubias A, Reyes J. 2009. Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress. Plant Molecular Biology 70, 385-401.
6. Aukerman MJ, Sakai H. 2003. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. The Plant Cell 15, 2730-2741. (Pubitemid 37470672)
7. Axtell MJ, Bartel DP. 2005. Antiquity of microRNAs and their targets in land plants. The Plant Cell 17, 1658-1673.
8. Axtell MJ, Bowman JL. 2008. Evolution of plant microRNAs and their targets. Trends in Plant Science 13, 343-349.
9. Bhalla PL, Singh MB. 2006. Molecular control of stem cell maintenance in shoot apical meristem. Plant Cell Reports 25, 249-256.
10. Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O. 2008. Widespread translational inhibition by plant miRNAs and siRNAs. Science 320, 1185-1190. (Pubitemid 351929501)
11. Brooks L III, Strable J, Zhang X, et al. 2009. Microdissection of shoot meristem functional domains. PLoS Genetics 5, e1000476.
12. Chuck G, Candela H, Hake S. 2009. Big impacts by small RNAs in plant development. Current Opinion in Plant Biology 12, 81-86.
13. Combier J-P, Frugier F, de Billy F, et al. 2006. MtHAP2-1 is a key transcriptional regulator of symbiotic nodule development regulated by microRNA169 in Medicago truncatula. Genes and Development 20, 3084-3088. (Pubitemid 44790624)
14. Garcia D, Collier SA, Byrne ME, Martienssen RA. 2006. Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway. Current Biology 16, 933-938.
15. Gardner PP, Daub J, Tate JG, et al. 2009. Rfam: Updates to the RNA families database. Nucleic Acids Research 37, D136-140.
16. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. 2008. miRBase: Tools for microRNA genomics. Nucleic Acids Research 36, D154-158. (Pubitemid 351149713)
17. Haerizadeh F, Wong CE, Singh MB, Bhalla PL. 2009. Genomewide analysis of gene expression in soybean shoot apical meristem. Plant Molecular Biology 69, 711-727.
18. Hwang H-W, Wentzel EA, Mendell JT. 2007. A hexanucleotide element directs microRNA nuclear import. Science 315, 97-100. (Pubitemid 46196987)
19. Jagadeeswaran G, Zheng Y, Li Y-F, et al. 2009. Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families. New Phytologist 184, 85-98.
20. Joshi T, Yan Z, Libault M, et al. 2010. Prediction of novel miRNAs and associated target genes in. Glycine max. BMC Bioinformatics 11, S14.
21. Juarez MT, Twigg RW, Timmermans MCP. 2004. Specification of adaxial cell fate during maize leaf development. Development 131, 4533-4544. (Pubitemid 39409694)
22. Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, Reski R, Frank W. 2010. Transcriptional control of gene expression by microRNAs. Cell 140, 111-122.
23. Kim JH, Choi DS, Kende H. 2003. The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in. Arabidopsis. The Plant Journal 36, 94-104. (Pubitemid 37231660)
24. Kim SW, Li Z, Moore PS, Monaghan AP, Chang Y, Nichols M, John B. 2010. A sensitive non-radioactive northern blot method to detect small RNAs. Nucleic Acids Research 38, e98.
25. Li W-X, Oono Y, Zhu J, He X-J, Wu J-M, Iida K, Lu X-Y, Cui X, Jin H, Zhu J- K. 2008. The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. The Plant Cell 20, 2238-2251. (Pubitemid 352844522)
26. Liang D, Wong CE, Singh MB, Beveridge CA, Phipson B, Smyth GK, Bhalla PL. 2009. Molecular dissection of the pea shoot apical meristem. Journal of Experimental Botany 60, 4201-4213.
27. Liu DM, Song Y, Chen ZX, Yu DQ. 2009a. Ectopic expression of miR396 suppresses GRF target gene expression and alters leaf growth in Arabidopsis. Physiologia Plantarum 136, 223-236.
28. Liu Q, Yao X, Pi L, Wang H, Cui X, Huang H. 2009b. The ARGONAUTE10 gene modulates shoot apical meristem maintenance and establishment of leaf polarity by repressing miR165/166 in. Arabidopsis. The Plant Journal 58, 27-40.
29. Mallory AC, Bartel DP, Bartel B. 2005. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. The Plant Cell 17, 1360-1375. (Pubitemid 43138190)
30. Mallory AC, Dugas DV, Bartel DP, Bartel B. 2004. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Current Biology 14, 1035-1046. (Pubitemid 38791565)
31. Mallory AC, Elmayan T, Vaucheret H. 2008. MicroRNA maturation and action - the expanding roles of ARGONAUTEs. Current Opinion in Plant Biology 11, 560-566.
32. Meyers BC, Axtell MJ, Bartel B, et al. 2008. Criteria for annotation of plant microRNAs. The Plant Cell 20, 3186-3190.
33. Nagasaki H, Itoh J-i Hayashi K, et al. 2007. The small interfering RNA production pathway is required for shoot meristem initiation in rice. Proceedings of the National Academy of Sciences, USA 104, 14867-14871. (Pubitemid 350003234)
34. Nogueira FTS, Chitwood DH, Madi S, Ohtsu K, Schnable PS, Scanlon MJ, Timmermans MCP. 2009. Regulation of small RNA accumulation in the maize shoot apex. PLoS Genetics 5, e1000320.
35. Nogueira FTS, Madi S, Chitwood DH, Juarez MT, Timmermans MCP. 2007. Two small regulatory RNAs establish opposing fates of a developmental axis. Genes and Development 21, 750-755. (Pubitemid 46572355)
36. Okamura K, Phillips MD, Tyler DM, Duan H, Chou Y-t Lai EC. 2008. The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nature Structural and Molecular Biology 15, 354-363. (Pubitemid 351483397)
37. Packer AN, Xing Y, Harper SQ, Jones L, Davidson BL. 2008. The bifunctional microRNA miR-9/miR-9* regulates REST and CoREST and is downregulated in Huntington's disease. Journal of Neuroscience 28, 14341-14346.
38. Palatnik JF, Allen E, Wu XL, Schommer C, Schwab R, Carrington JC, Weigel D. 2003. Control of leaf morphogenesis by microRNAs. Nature 425, 257-263. (Pubitemid 37158395)
39. Palatnik JF, Wollmann H, Schommer C, et al. 2007. Sequence and expression differences underlie functional specialization of ArabidopsismicroRNAs miR159 and miR319. Developmental Cell 13, 115-125. (Pubitemid 46972029)
40. Pant BD, Musialak-Lange M, Nuc P, May P, Buhtz A, Kehr J, Walther D, Scheible W- R. 2009. Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time PCR profiling and small RNA sequencing. Plant Physiology 150, 1541-55.
41. Politz JC, Hogan EM, Pederson T. 2009. MicroRNAs with a nucleolar location. RNA 15, 1705-1715.
42. Politz JC, Zhang F, Pederson T. 2006. MicroRNA-206 colocalizes with ribosome-rich regions in both the nucleolus and cytoplasm of rat myogenic cells. Proceedings of the National Academy of Sciences, USA 103, 18957-18962. (Pubitemid 350002810)
43. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsisthaliana. Genes and Development 20, 3407-3425. (Pubitemid 44969159)
44. Raman S, Greb T, Peaucelle A, Blein T, Laufs P, Theres K. 2008. Interplay of miR164 CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsisthaliana. The Plant Journal 55, 65-76. (Pubitemid 351990933)
45. Raventos D, Skriver K, Schlein M, Karnahl K, Rogers SW, Rogers JC, Mundy J. 1998. HRT, a novel zinc finger, transcriptional repressor from barley. Journal of Biological Chemistry 273, 23313-23320. (Pubitemid 28417518)
46. Rodriguez RE, Mecchia MA, Debernardi JM, Schommer C, Weigel D, Palatnik JF. 2010. Control of cell proliferation in Arabidopsisthaliana by microRNA miR396. Development 137, 103-112.
47. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP. 2006. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C-elegans. Cell 127, 1193-1207. (Pubitemid 44894525)
48. Singh MB, Bhalla PL. 2006. Plant stem cells carve their own niche. Trends in Plant Science 11, 241-246. (Pubitemid 43674088)
49. SiréC, Moreno AB, Garcia-Chapa M, López-Moya JJ, Segundo BS. 2009. Diurnal oscillation in the accumulation of Arabidopsis microRNAs, miR167, miR168, miR171 and miR398. FEBS Letters 583, 1039-1044.
50. Subramanian S, Fu Y, Sunkar R, Barbazuk WB, Zhu J-K, Yu O. 2008. Novel and nodulation-regulated microRNAs in soybean roots. BMC Genomics 9, 160.
51. Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MPS, Moulton V, Dalmay T. 2008. High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 9, 593.
52. Tucker MR, Laux T. 2007. Connecting the paths in plant stem cell regulation. Trends in Cell Biology 17, 403-410. (Pubitemid 47375103)
53. Vaucheret H, Vazquez F, Crete P, Bartel DP. 2004. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes and Development 18, 1187-1197. (Pubitemid 38669039)
54. Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY. 2005. Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. The Plant Cell 17, 2204-2216.
55. Wang Y, Li P, Cao X, Wang X, Zhang A, Li X. 2009. Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules. Biochemical and Biophysical Research Communications 378, 799-803.
56. Williams L, Grigg SP, Xie M, Christensen S, Fletcher JC. 2005. Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes. Development 132, 3657-3668. (Pubitemid 41301103)
57. Wong CE, Bhalla PL, Ottenhof H, Singh MB. 2008. Transcriptional profiling of the pea shoot apical meristem reveals processes underlying its function and maintenance. BMC Plant Biol 8, 73-84.
58. Wong CE, Singh MB, Bhalla PL. 2009. Molecular processes underlying the floral transition in the soybean shoot apical meristem. The Plant Journal 57, 832-845.
59. Wu G, Poethig RS. 2006. Temporal regulation of shoot development in Arabidopsisthaliana by miR156 and its target SPL3. Development 133, 3539-3547. (Pubitemid 44614278)
60. Wu M-F, Tian Q, Reed JW. 2006. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133, 4211-4218. (Pubitemid 44830665)
61. Xie ZX, Kasschau KD, Carrington JC. 2003. Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Current Biology 13, 784-789. (Pubitemid 36531029)
62. Zhang Y. 2005. miRU: An automated plant miRNA target prediction server. Nucleic Acids Research 33, W701-704. (Pubitemid 44530014)
63. Zhu QH, Spriggs A, Matthew L, Fan LJ, Kennedy G, Gubler F, Helliwell C. 2008. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Research 18, 1456-1465.
64. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31, 3406-3415. (Pubitemid 37442169)