The blossoming of RNA biology: Novel insights from plant systems

RNA

Volumn 12, Issue 12, 2006, Pages 2035-2046

  Bove, Jérôme ^a,c   Hord, Carey L H ^a,b,d   Mullen, Melissa A ^a,d  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c 208 Mueller Laboratory   (United States)

^d 104 Chemistry Bldg ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT RNA; SMALL INTERFERING RNA; TRANSFER RNA;

CONFERENCE PAPER; ENVIRONMENTAL FACTOR; GENE SEQUENCE; GENOME ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; PLANT DEVELOPMENT; PLANT GENETICS; PLANT PHYSIOLOGY; PLANT STRESS; PRIORITY JOURNAL; RNA PROCESSING;

GENE EXPRESSION REGULATION, PLANT; MOLECULAR BIOLOGY; PLANTS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, PLANT; SIGNAL TRANSDUCTION;

EID: 33845268223     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.303806     Document Type: Conference Paper

References (119)

1. Adenot, X., Elmayan, T., Lauressergues, D., Boutet, S., Bouche, N., Gasciolli, V., and Vaucheret, H. 2006. DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr. Biol. 16: 927-932.
2. Anandalakshmi, R., Pruss, G.J., Ge, X., Marathe, R., Mallory, A.C., Smith, T.H., and Vance, V.B. 1998. A viral suppressor of gene silencing in plants. Proc. Natl. Acad. Sci. 95: 13079-13084.
3. Aung, K., Lin, S.I., Wu, C.C., Huang, Y.T., Su, C.L., and Chiou, T.J. 2006. pho2, a phosphate overaccumulator, is caused by a nonsense mutation in a microRNA399 target gene. Plant Physiol. 141: 1000-1011.
4. Babitzke, P. and Gollnick, P. 2001. Posttranscription initiation control of tryptophan metabolism in Bacillus subtilis by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and RNA structure. J. Bacteriol. 183: 5795-5802.
5. Bae, W., Xia, B., Inouye, M., and Severinov, K. 2000. Escherichia coli CspA-family RNA chaperones are transcription antiterminators. Proc. Natl. Acad. Sci. 97: 7784-7789.
6. Bao, N., Lye, K.-W., 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.
7. Bari, R., Datt Pant, B., Stitt, M., and Scheible, W.R. 2006. PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol. 141: 988-999.
8. Batey, R.T., Gilbert, S.D., and Montange, R.K. 2004. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432: 411-415.
9. Benedetti, C.E., Xie, D., and Turner, J.G. 1995. Coi1-dependent expression of an Arabidopsis vegetative storage protein in flowers and siliques and in response to coronatine or methyl jasmonate. Plant Physiol. 109: 567-572.
10. Bezerra, I.C., Michaels, S.D., Schomburg, F.M., and Amasino, R.M. 2004. Lesions in the mRNA cap-binding gene ABA HYPERSENSITIVE 1 suppress FRIGIDA-mediated delayed flowering in Arabidopsis. Plant J. 40: 112-119.
11. Bollenbach, T.J., Lange, H., Gutierrez, R., Erhardt, M., Stern, D.B., and Gagliardi, D. 2005. RNR1, a 39-59 exoribonuclease belonging to the RNR superfamily, catalyzes 39 maturation of chloroplast ribosomal RNAs in Arabidopsis thaliana. Nucleic Acids Res. 33: 2751-2763.
12. 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.
13. Boutet, S., Vazquez, F., Liu, J., Beclin, C., Fagard, M., Gratias, A., Morel, J.B., Crete, P., Chen, X., and Vaucheret, H. 2003. Arabidopsis HEN1: A genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr. Biol. 13: 843-848.
14. Brennecke, J., Stark, A., Russell, R.B., and Cohen, S.M. 2005. Principles of microRNA-target recognition. PLoS Biol. 3: 404-418.
15. Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., et al. 2000. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18: 630-634.
16. Buttner, K., Wenig, K., and Hopfner, K.P. 2005. Structural framework for the mechanism of archaeal exosomes in RNA processing. Mol. Cell 20: 461-471.
17. Carmell, M.A., Xuan, Z., Zhang, M.Q., and Hannon, G.J. 2002. The Argonaute family: Tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes & Dev. 16: 2733-2742.
18. Chekanova, J.A., Dutko, J.A., Mian, I.S., and Belostotsky, D.A. 2002. Arabidopsis thaliana exosome subunit AtRrp4p is a hydrolytic 3′ → 5′ exonuclease containing S1 and KH RNA-binding domains. Nucleic Acids Res. 30: 695-700.
19. Chen, X. 2004. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025.
20. Chen, X. and Meyerowitz, E.M. 1999. HUA1 and HUA2 are two members of the floral homeotic AGAMOUS pathway. Mol. Cell 3: 349-360.
21. Chen, X., Liu, J., Cheng, Y., and Jia, D. 2002. HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development 129: 1085-1094.
22. Cheng, Y., Kato, N., Wang, W., Li, J., and Chen, X. 2003. Two RNA binding proteins, HEN4 and HUA1, act in the processing of AGAMOUS pre-mRNA in Arabidopsis thaliana. Dev. Cell 4: 53-66.
23. Chiou, T.J., Aung, K., Lin, S.I., Wu, C.C., Chiang, S.F., and Su, C.L. 2006. Regulation of phosphate homeostasis by microRNA in Arabidopsis. Plant Cell 18: 412-421.
24. Coen, E.S. and Meyerowitz, E.M. 1991. The war of the whorls: Genetic interactions controlling flower development. Nature 353: 31-37.
25. Crofts, A.J., Washida, H., Okita, T.W., Ogawa, M., Kumamaru, T., and Satoh, H. 2004. Targeting of proteins to endoplasmic reticulum-derived compartments in plants. The importance of RNA localization. Plant Physiol. 136: 3414-3419.
26. Crofts, A.J., Washida, H., Okita, T.W., Satoh, M., Ogawa, M., Kumamaru, T., and Satoh, H. 2005. The role of mRNA and protein sorting in seed storage protein synthesis, transport, and deposition. Biochem. Cell Biol. 83: 728-737.
27. Dalmay, T., Hamilton, A., Rudd, S., Angell, S., and Baulcombe, D.C. 2000. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101: 543-553.
28. Delaney, K.J., Xu, R., Zhang, J., Li, Q.Q., Yun, K.Y., Falcone, D.L., and Hunt, A.G. 2006. Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit. Plant Physiol. 140: 1507-1521.
29. Deleris, A., Gallego-Bartolome, J., Bao, J., Kasschau, K.D., Carrington, J.C., and Voinnet, O. 2006. Hierarchical action and inhibition of plant dicer-like proteins in antiviral defense. Science 313: 68-71.
30. Delhaize, E. and Randall, P.J. 1995. Characterization of a phosphate-accumulator mutant of Arabidopsis thaliana. Plant Physiol. 107: 207-213.
31. Deuschle, K., Funck, D., Forlani, G., Stransky, H., Biehl, A., Leister, D., van der Graaff, E., Kunze, R., and Frommer, W.B. 2004. The role of delta1-pyrroline-5-carboxylate dehydrogenase in proline degradation. Plant Cell 16: 3413-3425.
32. Deyholos, M.K., Cavaness, G.F., Hall, B., King, E., Punwani, J., Van Norman, J., and Sieburth, L.E. 2003. VARICOSE, a WD-domain protein, is required for leaf blade development. Development 130: 6577-6588.
33. Drews, G.N., Bowman, J.L., and Meyerowitz, E.M. 1991. Negative regulation of the Arabidopsis homeotic gene AGAMOUS by the APETALA2 product. Cell 65: 991-1002.
34. Ebhardt, H.A., Thi, E.P., Wang, M.B., and Unrau, P.J. 2005. Extensive 3′ modification of plant small RNAs is modulated by helper component-proteinase expression. Proc. Natl. Acad. Sci. 102: 13398-13403.
35. Ebhardt, H.A., Wiese, K.C., and Unrau, P.J. 2006. Ebbie: Automated analysis and storage of small RNA cloning data using a dynamic web server. BMC Bioinformatics 7: 185.
36. Emery, J.F., Floyd, S.K., Alvarez, J., Eshed, Y., Hawker, N.P., Izhaki, A., Baum, S.F., and Bowman, J.L. 2003. Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr. Biol. 13: 1768-1774.
37. Fahlgren, N., Montgomery, T.A., Howell, M.D., Allen, E., Dvorak, S.K., Alexander, A.L., and Carrington, J.C. 2006. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr. Biol. 16: 939-944.
38. Fang, L., Jiang, W., Bae, W., and Inouye, M. 1997. Promoterindependent cold-shock induction of cspA and its derepression at 37 degrees C by mRNA stabilization. Mol. Microbiol. 23: 355-364.
39. Farh, K.K., Grimson, A., Jan, C., Lewis, B.P., Johnston, W.K., Lim, L.P., Burge, C.B., and Bartel, D.P. 2005. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310: 1817-1821.
40. Fedoroff, N.V. 2002. RNA-binding proteins in plants: The tip of an iceberg? Curr. Opin. Plant Biol. 5: 452-459.
41. Fenger-Gron, M., Fillman, C., Norrild, B., and Lykke-Andersen, J. 2005. Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. Mol. Cell 20: 905-915.
42. Fujii, H., Chiou, T.J., Lin, S.I., Aung, K., and Zhu, J.K. 2005. A miRNA involved in phosphate-starvation response in Arabidopsis. Curr. Biol. 15: 2038-2043.
43. Garcia, D., Collier, S.A., Byrne, M.E., and Martienssen, R.A. 2006. Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway. Curr. Biol. 16: 933-938.
44. Goldstein, J., Pollitt, N.S., and Inouye, M. 1990. Major cold shock protein of Escherichia coli. Proc. Natl. Acad. Sci. 87: 283-287.
45. Grigg, S.P., Canales, C., Hay, A., and Tsiantis, M. 2005. SERRATE coordinates shoot meristem function and leaf axial patterning in Arabidopsis. Nature 437: 1022-1026.
46. Hamada, S., Ishiyama, K., Choi, S.-B., Wang, C., Singh, S., Kawai, N., Franceschi, V.R., and Okita, T.W. 2003a. The transport of prolamine RNAs to prolamine protein bodies in living rice endosperm cells. Plant Cell 15: 2253-2264.
47. Hamada, S., Ishiyama, K., Sakulsingharoj, C., Choi, S.B., Wu, Y., Wang, C., Singh, S., Kawai, N., Messing, J., and Okita, T.W. 2003b. Dual regulated RNA transport pathways to the cortical region in developing rice endosperm. Plant Cell 15: 2265-2272.
48. Hellmann, H., Funck, D., Rentsch, D., and Frommer, W.B. 2000. Hypersensitivity of an Arabidopsis sugar signaling mutant toward exogenous proline application. Plant Physiol. 123: 779-789.
49. Henderson, I.R., Liu, F., Drea, S., Simpson, G.G., and Dean, C. 2005. An allelic series reveals essential roles for FY in plant development in addition to flowering-time control. Development 132: 3597-3607.
50. Henderson, I.R., Zhang, X., Lu, C., Johnson, L., Meyers, B.C., Green, P.J., and Jacobsen, S.E. 2006. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat. Genet. 38: 721-725.
51. Hudson, A. 2000. Development of symmetry in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 51: 349-370.
52. Hugouvieux, V., Kwak, J.M., and Schroeder, J.I. 2001. An mRNA cap binding protein, ABH1, modulates early abscisic acid signal transduction in Arabidopsis. Cell 106: 477-487.
53. 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.
54. Karlson, D., Nakaminami, K., Toyomasu, T., and Imai, R. 2002. A cold-regulated nucleic acid-binding protein of winter wheat shares a domain with bacterial cold shock proteins. J. Biol. Chem. 277: 35248-35256.
55. Keene, J.D. and Tenenbaum, S.A. 2002. Eukaryotic mRNPs may represent posttranscriptional operons. Mol. Cell 9: 1161-1167.
56. Keene, J.D., Komisarow, J.M., and Friedersdorf, M.B. 2006. RIP-Chip: The isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat. Protocols 1: 302-307.
57. Krek, A., Grun, D., Poy, M.N., Wolf, R., Rosenberg, L., Epstein, E.J., MacMenamin, P., da Piedade, I., Gunsalus, K.C., Stoffel, M., et al. 2005. Combinatorial microRNA target predictions. Nat. Genet. 37: 495-500.
58. Kurihara, Y. and Watanabe, Y. 2004. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. 101: 12753-12758.
59. Leung, A.K., Trinkle-Mulcahy, L., Lam, Y.W., Andersen, J.S., Mann, M., and Lamond, A.I. 2006. NOPdb: Nucleolar proteome database. Nucleic Acids Res. 34: D218-D220.
60. Lewis, B.P., Burge, C.B., and Bartel, D.P. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
61. Li, H., Xu, L., Wang, H., Yuan, Z., Cao, X., Yang, Z., Zhang, D., Xu, Y., and Huang, H. 2005a. The Putative RNA-dependent RNA polymerase RDR6 acts synergistically with ASYMMETRIC LEAVES1 and 2 to repress BREVIPEDICELLUS and MicroRNA165/166 in Arabidopsis leaf development. Plant Cell 17: 2157-2171.
62. Li, J., Yang, Z., Yu, B., Liu, J., and Chen, X. 2005b. Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr. Biol. 15: 1501-1507.
63. Lim, L.P., Lau, N.C., Weinstein, E.G., Abdelhakim, A., Yekta, S., Rhoades, M.W., Burge, C.B., and Bartel, D.P. 2003. The micro-RNAs of Caenorhabditis elegans. Genes & Dev. 17: 991-1008.
64. Lingel, A., Simon, B., Izaurralde, E., and Sattler, M. 2003. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426: 465-469.
65. Liu, J., Carmell, M.A., Rivas, F.V., Marsden, C.G., Thomson, J.M., Song, J.J., Hammond, S.M., Joshua-Tor, L., and Hannon, G.J. 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437-1441.
66. Lu, C. and Fedoroff, N. 2000. A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin. Plant Cell 12: 2351-2366.
67. 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.
68. Ma, H. 2005. Molecular genetic analyses of microsporogenesis and microgametogenesis in flowering plants. Annu. Rev. Plant Biol. 56: 393-434.
69. Macknight, R., Bancroft, I., Page, T., Lister, C., Schmidt, R., Love, K., Westphal, L., Murphy, G., Sherson, S., Cobbett, C., et al. 1997. FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains. Cell 89: 737-745.
70. Macknight, R., Duroux, M., Laurie, R., Dijkwel, P., Simpson, G., and Dean, C. 2002. Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA. Plant Cell 14: 877-888.
71. Mallory, A.C., Reinhart, B.J., Jones-Rhoades, M.W., Tang, G., Zamore, P.D., Barton, M.K., and Bartel, D.P. 2004. MicroRNA control of PHABULOSA in leaf development: Importance of pairing to the microRNA 59 region. EMBO J. 23: 3356-3364.
72. Mandal, M. and Breaker, R.R. 2004. Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol. 5: 451-463.
73. Mandal, M., Boese, B., Barrick, J.E., Winkler, W.C., and Breaker, R.R. 2003. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113: 577-586.
74. Margis, R., Fusaro, A.F., Smith, N.A., Curtin, S.J., Watson, J.M., Finnegan, E.J., and Waterhouse, P.M. 2006. The evolution and diversification of Dicers in plants. FEBS Lett. 580: 2442-2450.
75. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
76. McConnell, J.R. and Barton, M.K. 1998. Leaf polarity and meristem formation in Arabidopsis. Development 125: 2935-2942.
77. 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.
78. Michaels, S.D. and Amasino, R.M. 1999. FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11: 949-956.
79. Montange, R.K. and Batey, R.T. 2006. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441: 1172-1175.
80. Mourrain, P., Beclin, C., Elmayan, T., Feuerbach, F., Godon, C., Morel, J.B., Jouette, D., Lacombe, A.M., Nikic, S., Picault, N., et al. 2000. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101: 533-542.
81. Nakaminami, K., Sasaki, K., Kajita, S., Takeda, H., Karlson, D., Ohgi, K., and Imai, R. 2005. Heat stable ssDNA/RNA-binding activity of a wheat cold shock domain protein. FEBS Lett. 579: 4887-4891.
82. Nudler, E. 2006. Flipping riboswitches. Cell 126: 19-22.
83. Park, W., Li, J., Song, R., Messing, J., and Chen, X. 2002. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12: 1484-1495.
84. Pendle, A.F., Clark, G.P., Boon, R., Lewandowska, D., Lam, Y.W., Andersen, J., Mann, M., Lamond, A.I., Brown, J.W., and Shaw, P.J. 2005. Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Mol. Biol. Cell 16: 260-269.
85. Peragine, A., Yoshikawa, M., Wu, G., Albrecht, H.L., and Poethig, R.S. 2004. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes & Dev. 18: 2368-2379.
86. Perrin, R., Lange, H., Grienenberger, J.M., and Gagliardi, D. 2004. AtmtPNPase is required for multiple aspects of the 18S rRNA metabolism in Arabidopsis thaliana mitochondria. Nucleic Acids Res. 32: 5174-5182.
87. Quesada, V., Macknight, R., Dean, C., and Simpson, G.G. 2003. Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. EMBO J. 22: 3142-3152.
88. Rehmsmeier, M., Steffen, P., Hochsmann, M., and Giegerich, R. 2004. Fast and effective prediction of microRNA/target duplexes. RNA 10: 1507-1517.
89. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., and Bartel, D.P. 2002. MicroRNAs in plants. Genes & Dev. 16: 1616-1626.
90. Roth, B.M., Pruss, G.J., and Vance, V.B. 2004. Plant viral suppressors of RNA silencing. Virus Res. 102: 97-108.
91. Schmitz-Linneweber, C., Williams-Carrier, R., and Barkan, A. 2005. RNA immunoprecipitation and microarray analysis show a chloroplast Pentatricopeptide repeat protein to be associated with the 5′ region of mRNAs whose translation it activates. Plant Cell 17: 2791-2804.
92. Shamovsky, I., Ivannikov, M., Kandel, E.S., Gershon, D., and Nudler, E. 2006. RNA-mediated response to heat shock in mammalian cells. Nature 440: 556-560.
93. Siegfried, K.R., Eshed, Y., Baum, S.F., Otsuga, D., Drews, G.N., and Bowman, J.L. 1999. Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. Development 126: 4117-4128.
94. Simpson, G.G. and Dean, C. 2002. Arabidopsis, the Rosetta stone of flowering time? Science 296: 285-289.
95. Simpson, G.G., Dijkwel, P.P., Quesada, V., Henderson, I., and Dean, C. 2003. FY is an RNA 39 end-processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell 113: 777-787.
96. Song, J.J., Liu, J., Tolia, N.H., Schneiderman, J., Smith, S.K., Martienssen, R.A., Hannon, G.J., and Joshua-Tor, L. 2003. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat. Struct. Biol. 10: 1026-1032.
97. Song, J.J., Smith, S.K., Hannon, G.J., and Joshua-Tor, L. 2004. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305: 1434-1437.
98. Sudarsan, N., Barrick, J.E., and Breaker, R.R. 2003. Metabolitebinding RNA domains are present in the genes of eukaryotes. RNA 9: 644-647.
99. Sunkar, R. and Zhu, J.K. 2004. Novel and stress-regulated micro-RNAs and other small RNAs from Arabidopsis. Plant Cell 16: 2001-2019.
100. 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.
101. Thore, S., Leibundgut, M., and Ban, N. 2006. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312: 1208-1211.
102. Van de Bor, V. and Davis, I. 2004. mRNA localisation gets more complex. Curr. Opin. Cell Biol. 16: 300-307.
103. Walter, M., Kilian, J., and Kudla, J. 2002. PNPase activity determines the efficiency of mRNA 3′-end processing, the degradation of tRNA and the extent of polyadenylation in chloroplasts. EMBO J. 21: 6905-6914.
104. Weigel, D. and Meyerowitz, E.M. 1994. The ABCs of floral homeotic genes. Cell 78: 203-209.
105. Western, T.L., Cheng, Y., Liu, J., and Chen, X. 2002. HUA ENHANCER2, a putative DExH-box RNA helicase, maintains homeotic B and C gene expression in Arabidopsis. Development 129: 1569-1581.
106. Winkler, W.C. and Breaker, R.R. 2003. Genetic control by metabolite-binding riboswitches. ChemBioChem 4: 1024-1032.
107. Wurschum, T., Gross-Hardt, R., and Laux, T. 2006. APETALA2 regulates the stem cell niche in the Arabidopsis shoot meristem. Plant Cell 18: 295-307.
108. 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.
109. Xu, L., Xu, Y., Dong, A., Sun, Y., Pi, L., and Huang, H. 2003. Novel as1 and as2 defects in leaf adaxial-abaxial polarity reveal the requirement for ASYMMETRIC LEAVES1 and 2 and ERECTA functions in specifying leaf adaxial identity. Development 130: 4097-4107.
110. Xu, L., Yang, L., Pi, L., Liu, Q., Ling, Q., Wang, H., Poethig, R.S., and Huang, H. 2006. Genetic interaction between the AS1-AS2 and RDR6-SGS3-AGO7 pathways for leaf morphogenesis. Plant Cell Physiol. 47: 853-863.
111. Yamada, K., Lim, J., Dale, J.M., Chen, H., Shinn, P., Palm, C.J., Southwick, A.M., Wu, H.C., Kim, C., Nguyen, M., et al. 2003. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302: 842-846.
112. Yan, K.S., Yan, S., Farooq, A., Han, A., Zeng, L., and Zhou, M.M. 2003. Structure and conserved RNA binding of the PAZ domain. Nature 426: 468-474.
113. Yang, L., Huang, W., Wang, H., Cai, R., Xu, Y., and Huang, H. 2006a. Characterizations of a hypomorphic argonaute1 mutant reveal novel AGO1 functions in Arabidopsis lateral organ development. Plant Mol. Biol. 61: 63-78.
114. Yang, L., Liu, Z., Lu, F., Dong, A., and Huang, H. 2006b. SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J. (in press).
115. Yanofsky, M.F., Ma, H., Bowman, J.L., Drews, G.N., Feldmann, K.A., and Meyerowitz, E.M. 1990. The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature 346: 35-39.
116. Yu, B., Yang, Z., Li, J., Minakhina, S., Yang, M., Padgett, R.W., Steward, R., and Chen, X. 2005a. Methylation as a crucial step in plant microRNA biogenesis. Science 307: 932-935.
117. Yu, J.H., Yang, W.H., Gulick, T., Bloch, K.D., and Bloch, D.B. 2005b. Ge-1 is a central component of the mammalian cytoplasmic mRNA processing body. RNA 11: 1795-1802.
118. Zhong, R. and Ye, Z.H. 2004. amphivasal vascular bundle 1, a gain-of-function mutation of the IFL1/REV gene, is associated with alterations in the polarity of leaves, stems and carpels. Plant Cell Physiol. 45: 369-385.
119. Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L., and Gruissem, W. 2004. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 136: 2621-2632.