siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis

Genes and Development

Volumn 18, Issue 23, 2004, Pages 2873-2878

  Liu, Jun ^a,c   He, Yuehui ^b   Amasino, Richard ^b   Chen, Xuemei ^a  

^a RUTGERS UNIVERSITY   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c SHANGHAI UNIVERSITY   (China)

Author keywords

FLC; H3 K9 methylation; HEN1; Intron; siRNA; Transposon

Indexed keywords

ALLELE; ARABIDOPSIS; ARTICLE; CHROMATIN; CONTROLLED STUDY; EUKARYOTE; FLOWERING; GENE CONTROL; GENE EXPRESSION; GENE LOCUS; GENE TARGETING; GENOME; INTRON; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; TRANSPOSON;

ARABIDOPSIS; BASE SEQUENCE; DNA PRIMERS; DNA TRANSPOSABLE ELEMENTS; IMMUNOPRECIPITATION; INTRONS; RNA, SMALL INTERFERING;

ARABIDOPSIS; EMBRYOPHYTA; EUKARYOTA; TRANSPOSONS;

EID: 10044244768     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.1217304     Document Type: Article

References (39)

1. Bartee, L., Malagnac, F., and Bender, J. 2001. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes & Dev. 15: 1753-1758.
2. Bartel, D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
3. Boss, P.K., Bastow, R.M., Mylne, J.S., and Dean, C. 2004. Multiple pathways in the decision to flower: Enabling, promoting, and resetting. Plant Cell 16 Suppl: S18-S31.
4. Boutet, S., Vazquez, F., Liu, J., Beclin, C., Fagard, M., Gratias, A., Morel, I.E., 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.
5. 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.
6. 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.
7. Finnegan, E.J., Margis, R., and Waterhouse, P.M. 2003. Posttranscriptional gene silencing is not compromised in the Arabidopsis carpel factory (dicer-like1) mutant, a homolog of Dicer-1 from Drosophila. Curr. Biol. 13: 236-240.
8. Gazzani, S., Gendall, A.R., Lister, C., and Dean, C. 2003. Analysis of the molecular basis of flowering time variation in Arabidopsis accessions. Plant Physiol. 132: 1107-1114.
9. Grover, D., Mukerji, M., Bhatnagar, P., Kannan, K., and Brahmachari, S.K. 2004. Alu repeat analysis in the complete human genome: Trends and variations with respect to genomic composition. Bioinformatics 20: 813-817.
10. Hall, I.M., Shankaranarayana, G.D., Noma, K., Ayoub, N., Cohen, A., and Grewal, S.I. 2002. Establishment and maintenance of a heterochromatin domain. Science 297: 2232-2237.
11. Hamilton, A.J. and Baulcombe, D.C. 1999. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286: 950-952.
12. Hamilton, A., Voinnet, O., Chappell, L., and Baulcombe, D. 2002. Two classes of short interfering RNA in RNA silencing. EMBO J. 21: 4671-4679.
13. Hannon, G.J. 2002. RNA interference. Nature 418: 244-251.
14. He, Y., Michaels, S., and Amasino, R. 2003. Regulation of flowering time by histone acetylation in Arabidopsis. Science 302: 1751-1754.
15. Johanson, U., West, J., Lister, C., Michaels, S., Amasino, R., and Dean, C. 2000. Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science 290: 344-347.
16. Johnson, L., Cao, X., and Jacobsen, S. 2002. Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr. Biol. 12: 1360-1367.
17. Lee, I., Bleecker, A., and Amasino, R.M. 1993a. Analysis of naturally occurring late flowering in Arabidopsis thaliana. Mol. Gen. Genet. 237: 171-176.
18. Lee, R.C., Feinbaum, R.L., and Ambros, V. 1993b. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
19. Lindroth, A.M., Cao, X., Jackson, J.P., Zilberman, D., McCallum, C.M., Henikoff, S., and Jacobsen, S.E. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292: 2077-2080.
20. Lippman, Z., Gendrel, A.V., Black, M., Vaughn, M.W., Dedhia, N., McCombie, W.R., Lavine, K., Mittal, V., May, B., Kasschau, K.D., et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
21. McClintock, B. 1950. The origin and behavior of mutable loci in maize. Proc. Natl. Acad. Sci. 36: 344-355,
22. 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.
23. _. 2001. Loss of FLOWERING LOCUS C activity eliminates the late-flowering phenotype of FRIGIDA and autonomous pathway mutations but not responsiveness to vernalization. Plant Cell 13: 935-941.
24. Michaels, S., He, Y., Scortecci, K.C., and Amasino, R. 2003. Attenuation of FLOWERING LOCUS C activity as a mechanism for the evolution of summer-annual flowering behavior in Arabidopsis. Proc. Natl. Acad. Sci. 100: 10102-10107.
25. 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.
26. Nekrutenko, A. and Li, W.-H. 2001. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 17: 619-621.
27. 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.
28. Plasterk, R.H. 2002. RNA silencing: The genome's immune system. Science 296: 1263-1265.
29. Ray, A., Lang, J.D., Golden, T., and Ray, S. 1996. SHORT INTEGUMENT (SIN1), a gene required for ovule development in Arabidopsis, also controls flowering time. Development 122: 2631-2638.
30. Reinhart, B.J. and Bartel, D.P. 2002. Small RNAs correspond to centromere heterochromatic repeats. Science 297: 1831.
31. Reinhart, B.J., Slack, F.J., Basson, M., Pasquinelli, A.E., Bettinger, J.C., Rougvie, A.E., Horvitz, H.R., and Ruvkun, G. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
32. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., and Bartel, D.P. 2002. MicroRNAs in plants. Genes & Dev. 16: 1616-1626.
33. Rouse, D.T., Sheldon, C.C., Bagnall, D.J., Peacock, W.J., and Dennis, E.S. 2002. FLC, a repressor of flowering, is regulated by genes in different inductive pathways. Plant J. 29: 183-191.
34. Sheldon, C.C., Burn, J.E., Perez, P.P., Metzger, J., Edwards, J.A., Peacock, W.J., and Dennis, E.S. 1999. The FLF MADS box gene: A repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11: 445-458.
35. Sheldon, C.C., Conn, A.B., Dennis, E.S., and Peacock, W.J. 2002. Different regulatory regions are required for the vernalization-induced repression of FLOWERING LOCUS C and for the epigenetic maintenance of repression. Plant Cell 14: 2527-2537.
36. Volpe, T.A., Kidner, C., Hall, I.M., Teng, G., Grewal, S.I., and Martienssen, R.A. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297: 1833-1837.
37. Weil, C.F. and Wessler, S.R. 1990. The effects of plant transposable element insertion on transcription initiation and RNA processing. Annu. Rev. Plant Physiol. Plant Mol. Biol. 41: 527-552.
38. 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: e107.
39. 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.