microRNAs in seeds: Modified detection techniques and potential applications

Canadian Journal of Botany

Volumn 84, Issue 2, 2006, Pages 189-198

  Martin, Ruth C ^a,b   Liu, Po Pu ^a   Nonogaki, Hiroyuki ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Arabidopsis; Development; Germination; Lycopersicon esculentum; microRNA; Seeds

Indexed keywords

PLANTS (BOTANY); RNA; SEED; TISSUE;

ARABIDOPSIS; DEVELOPMENT; GERMINATION; LYCOPERSICON ESCULENTUM; MICRORNA;

GENETIC ENGINEERING;

GENE EXPRESSION; GERMINATION; RNA; SEED;

GENES; GENETIC ENGINEERING; PLANTS; SEEDS; TISSUE;

EID: 33745652452     PISSN: 00084026     EISSN: None     Source Type: Journal    
DOI: 10.1139/B05-141     Document Type: Conference Paper

References (72)

1. Achard, P., Herr, A., Baulcombe, D.C., and Harberd, N.P. 2004. Modulation of floral development by a gibberellin-regulated microRNA. Development, 131: 3357-3365. doi: 10.1242/dev.01206.
2. Aida, M., Ishida, T., Fukaki, H., Fujisawa, H., and Tasaka, M. 1997. Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell, 9: 841-857. doi: 10.1105/tpc.9.6.841.
3. 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. doi: 10.1016/j.cell.2005.04.004.
4. Aukerman, M.J., and Sakai, H. 2003. Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell, 15: 2730-2741. doi: 10.1105/tpc.016238.
5. Axtell, M.J., and Bartel, D.P. 2005. Antiquity of microRNAs and their targets in land plants. Plant Cell, 17: 1658-1673. doi: 10.1105/tpc.105.032185.
6. Babak, T., Zhang, W., Morris, Q., Blencowe, B.J., and Hughes, T.R. 2004. Probing microRNAs with microarrays: tissue specificity and functional inference. RNA, 10: 1813-1819. doi: 10.1261/rna.7119904.
7. Baker, C.C., Sieber, P., Wellmer, F., and Meyerowitz, E.M. 2005. The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Curr. Biol. 15: 303-315. doi: 10.1016/j.cub.2005. 02.017.
8. Bao, N., Khar-wai, L., and Barton, M.K. 2004. MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Dev. Cell, 7: 653-662. doi: 10.1016/j.devcel.2004.10.003.
9. Baskerville, S., and Bartel, D.P. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA, 11: 241-247. doi: 10.1261/rna.7240905.
10. Billoud, B., De Paepe, R., Baulcombe, D., and Boccara, M. 2005. Identification of new small non-coding RNAs from tobacco and Arabidopsis. Biochimie, 87: 905-910. doi: 10.1016/j.biochi.2005.06.001.
11. Bonnet, E., Wuyts, J., Rouze, P., and Van de Peer, Y. 2004. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc. Natl. Acad. Sci. USA, 101: 11511-11516. doi: 10.1073/pnas.0404025101.
12. Calin, G.A., Liu, C.G., Sevignani, C., Ferracin, M., Felli, N., Dumitru, C.D., Shimizu, M., Cimmino, A., Zupo, S., Dono, M., Dell'Aquila, M.L., Alder, H., Rassenti, L., Kipps, T.J., Bullrich, F., Negrini, M., and Croce, C.M. 2004. MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc. Natl. Acad. Sci. USA, 101: 11755-11760. doi: 10.1073/pnas.0404432101.
13. Chen, X. 2004. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 303: 2022-2025. doi: 10.1126/science.1088060.
14. Cubas, P., Lauter, N., Doebley, J., and Coen, E. 1999. The TCP domain: a motif found in proteins regulating plant growth and development. Plant J. 18: 215-222. doi: 10.1046/j.1365-313X.1999.00444.x.
15. Dharmasiri, N., Dharmasiri, S., and Estelle, M. 2005. The F-box protein TIR1 is an auxin receptor. Nature (London), 435: 441-445. doi: 10.1038/nature03543.
16. Floyd, S.K., and Bowman, J.L. 2004. Gene regulation: ancient microRNA target sequences in plants. Nature (London), 428: 485-486. doi: 10.1038/428485a.
17. Guo, H.S., Xie, Q., Fei, J.F., and Chua, N.H. 2005. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to down-regulate auxin signals for Arabidopsis lateral root development. Plant Cell, 17: 1376-1386. doi: 10.1105/tpc.105.030841.
18. Jofuku, K.D., den Boer, B.G., Van Montagu, M., and Okamuro, J.K. 1994. Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell, 6: 1211-1225. doi: 10.1105/tpc.6.9.1211.
19. Jofuku, K.D., Omidyar, P.K., Gee, Z., and Okamuro, J.K. 2005. Control of seed mass and seed yield by the floral homeotic gene APETALA2. Proc. Natl. Acad. Sci. USA, 102: 3117-3122. doi: 10.1073/pnas.0409893102.
20. Johnson, S.M., Lin, S.Y., and Slack, F.J. 2003. The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Dev. Biol. 259: 364-379.
21. 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.
22. Juarez, M.T., Kui, J.S., Thomas, J., Heller, B.A., and Timmermans, M.C. 2004. MicroRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature (London), 428: 84-88. doi: 10.1038/nature02363.
23. Kasschau, K.D., Xie, Z., Allen, E., Llave, C., Chapman, E.J., Krizan, K.A., and Carrington, J.C. 2003. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev. Cell, 4: 205-217. doi: 10.1016/S1534-5807(03)00025-X.
24. Kepinski, S., and Leyser, O. 2005. The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature (London), 435: 446-451. doi: 10.1038/nature03542.
25. Kim, J., Jung, J.H., Reyes, J.L., Kim, Y.S., Kim, S.Y., Chung, K.S., Kim, J.A., Lee, M., Lee, Y., Narry Kim, V., Chua, N.H., and Park, C.M. 2005. microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J. 42: 84-94. doi: 10.1111/j.1365-313X. 2005.02354.x.
26. Koornneef, M., Luiten, W., de Vlaming, P., and Schram, A.W. 1982. A gene controlling flavonoid-3′-hydroxylation in Arabidopsis. Arabidopsis Inf. Serv. 19: 113-115.
27. Kurihara, Y., and Watanabe, Y. 2004. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. USA, 101: 12753-12758. doi: 10.1073/pnas.0403115101.
28. Laufs, P., Peaucelle, A., Morin, H., and Traas, J. 2004. MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development, 131: 4311-4322. doi: 10.1242/dev.01320.
29. Lauter, N., Kampani, A., Carlson, S., Goebel, M., and Moose, S.P. 2005. microRNA172 down-regulates glossy 15 to promote vegetative phase change in maize. Proc. Natl. Acad. Sci. USA, 102: 9412-9417. doi: 10.1073/pnas.0503927102.
30. Lee, R.C., Feinbaum, R.L., and Ambros, V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with anti-sense complementarity to lin-14. Cell, 75: 843-854. doi: 10.1016/0092-8674(93)90529-Y.
31. Lee, Y., Ahn, C., Ahn, J., Choi, H., Han, J., Hyounjeong, C., Kim, J., Yim, J., Lee, J., Provost, P., Radmark, O., Kim, S., and Kim, V. 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature (London), 425: 415-419. doi: 10.1038/nature01957.
32. Lee, Y., Kim, M., Han, J., Yeom, K.H., Lee, S., Baek, S.H., and Kim, V.N. 2004. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23: 4051-4060 . doi: 10.1038/sj.emboj.7600385.
33. 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. doi: 10.1093/nar/gni019.
34. Lim, L.P., Lau, N.C., Garrett-Engele, P., Grimson, A., Schelter, J.M., Castle, J., Bartel, D.P., Linsley, P.S., and Johnson, J.M. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature (London), 433: 769-773. doi: 10.1038/nature03315.
35. Liu, P.P., Koizuka, N., Homrichhausen, T.M., Hewitt, J.R., Martin, R.C., and Nonogaki, H. 2005a. Large-scale screening of Arabidopsis enhancer-trap lines for seed germination-associated genes. Plant J. 41: 936-944. doi: 10.1111/j.1365-313X.2005.02347.x.
36. Liu, P.-P., Koizuka, N., Martin, R.C., and Nonogaki, H. 2005b. The BME3 (Blue Micropylar End 3) GATA zinc finger transcription factor is a positive regulator of Arabidopsis seed germination. Plant J. 44: 960-971.
37. 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 (Washington, D.C.), 297: 2053-2056. doi: 10.1126/science.1076311.
38. 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. doi: 10.1105/tpc.105. 033456.
39. Mallory, A.C., Dugas, D.V., Bartel, D.P., and Bartel, B. 2004. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr. Biol. 14: 1035-1046. doi: 10.1016/j.cub.2004.06.022.
40. Mallory, A.C., Bartel, D.P., and Bartel, B. 2005. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell, 17: 1360-1375. doi: 10.1105/tpc.105.031716.
41. Martin, R.C., Liu, P.-P., and Nonogaki, H. 2005. Simple purification of small RNAs from seeds and efficient detection of multiple microRNAs expressed in Arabidopsis thaliana and tomato (Lycopersicon esculentum) seeds. Seed Sci. Res. 15: 319-328.
42. McConnell, J.R., Emery, J., Eshed, Y., Bao, N., Bowman, J., and Barton, M.K. 2001. Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. Nature, 411: 709-713. doi: 10.1038/35079635.
43. Millar, A.A., and Gubler, F. 2005. The Arabidopsis GAMYB-Like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell, 17: 705-721. doi: 10.1105/tpc.104.027920.
44. Miska, E.A., Alvarez-Saavedra, E., Townsend, M., Yoshii, A., Sestan, N., Rakic, P., Constantine-Paton, M., and Horvitz, H.R. 2004. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 5: R68.
45. Nath, U., Crawford, B.C., Carpenter, R., and Coen, E. 2003. Genetic control of surface curvature. Science, 299: 1404-1407. doi: 10.1126/science. 1079354.
46. Nonogaki, H., and Bradford, K.J. 2003. Tissue printing for localization of mRNA expression in seeds. In The biology of seeds: Recent research advances. Edited by K.J. Bradford, D. Come, G. Nicolas, and H. Pritchard. CAB International, Wallingford, UK. pp. 171-179.
47. Ohto, M.A., Fischer, R.L., Goldberg, R.B., Nakamura, K., and Harada, J.J. 2005. Control of seed mass by APETALA2. Proc. Natl. Acad. Sci. USA, 102: 3123-3128. doi: 10.1073/pnas.0409858102.
48. Okushima, Y., Overvoorde, P.J., Arima, K., Alonso, J.M., Chan, A., Chang, C., Ecker, J.R., Hughes, B., Lui, A., Nguyen, D., Onodera, C., Quach, H., Smith, A., Yu, G., and Theologis, A. 2005. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell, 17: 444-463. doi: 10.1105/tpc.104.028316.
49. Palatnik, J.F., Allen, E., Wu, X., Schommer, C., Schwab, R., Carrington, J.C., and Weigel, D. 2003. Control of leaf morphogenesis by microRNAs. Nature (London), 425: 257-263. doi: 10.1038/nature01958.
50. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., and Bartel, D.P. 2002. MicroRNAs in plants. Genes Dev. 16: 1616-1626. doi: 10.1101/gad.1004402.
51. 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. doi: 10.1016/S0092-8674(02)00863-2.
52. Sambrook, J., Fritsch, E.F., and Maniatis, T. 1989. Molecular cloning: A laboratory manual. 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
53. Schauer, S.E., Jacobsen, S.E., Meinke, D.W., and Ray, A. 2002. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci. 7: 487-491. doi: 10.1016/S1360-1385(02)02355-5.
54. Schmittgen, T.D., Jiang, J., Liu, Q., and Yang, L. 2004. A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res. 32: e43. doi: 10.1093/nar/gnh040.
55. 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. doi: 10.1016/j.devcel.2005.01.018.
56. Stone, J.M., Liang, X., Nekl, E.R., and Stiers, J.J. 2005. Arabidopsis AtSPL14, a plant-specific SBP-domain transcription factor, participates in plant development and sensitivity to fumonisin B1. Plant J. 41: 744-754. doi: 10.1111/j.1365-313X.2005.02334.x.
57. Sunkar, R., and Zhu, J.K. 2004. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 16: 2001-2019. doi: 10.1105/tpc.104.022830.
58. Sunkar, R., Girke, T., Jain, P., and Zhu, J. 2005. Cloning and characterization of microRNAs from rice. Plant Cell, 17: 1397-1411. doi: 10.1105/tpc.105.031682.
59. Takada, S., Hibara, K., Ishida, T., and Tasaka, M. 2001. The CUP-SHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation. Development, 128: 1127-1135.
60. Tang, G., Reinhart, B.J., Bartel, D.P., and Zamore, P.D. 2003. A biochemical framework for RNA silencing in plants. Genes Dev. 17: 49-63. doi: 10.1101/gad.1048103.
61. 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. doi: 10.1038/nmeth704.
62. Tomari, Y., and Zamore, P.D. 2005. Perspective: machines for RNAi. Genes Dev. 19: 517-529. doi: 10.1101/gad.1284105.
63. Unte, U.S., Sorensen, A.M., Pesaresi, P., Gandikota, M., Leister, D., Saedler, H., and Huijser, P. 2003. SPL8, an SBP-box gene that affects pollen sac development in Arabidopsis. Plant Cell, 15: 1009-1019. doi: 10.1105/tpc.010678.
64. Vazquez, F., Gasciolli, V., Crete, P., and Vaucheret, H. 2004. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol. 14: 346-351. doi: 10.1016/S0960-9822(04)00047-8.
65. Vaucheret, H., Vazquez, F., Crete, P., and Bartel, D.P. 2004. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev. 18: 1187-1197. doi: 10.1101/gad.1201404.
66. 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. doi: 10.1093/nar/gkh332.
67. 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. doi: 10.1105/tpc.105.033076.
68. Weigel, D., Ahn, J.H., Blazquez, M.A., Borevitz, J.O., Christensen, S.K., Fankhauser, C., Ferrandiz, C., Kardailsky, I., Malancharuvil, E.J., Neff, M.M., Nguyen, J.T., Sato, S., Wang, Z.Y., Xia, Y., Dixon, R.A., Harrison, M.J., Lamb, C.J., Yanofsky, M.F., and Chory, J. 2000. Activation tagging in Arabidopsis. Plant Physiol. 122: 1003-1013. doi: 10.1104/pp.122.4.1003.
69. 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. doi: 10.1073/pnas.0504029102.
70. Xie, Z., Johansen, L., Gustafson, A., Kasschau, K., Lellis, A., Zilberman, D., Jacobsen, S., and Carrington, J. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2: E104. doi: 10.1371/journal.pbio.0020104.
71. Yekta, S., Shih, I.H., and Bartel, D.P. 2004. MicroRNA-directed cleavage of HOXB8 mRNA. Science (Washington, D.C.), 304: 594-596. doi: 10.1126/science.1097434.
72. 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. doi: 10.1038/sj.cr.7290302.