Expression of the rice microRNA miR820 is associated with epigenetic modifications at its own locus

Genes and Genetic Systems

Volumn 88, Issue 2, 2013, Pages 105-112

  Nosaka, Misuzu ^a   Ono, Akemi ^a   Ishiwata, Aiko ^a   Shimizu Sato, Sae ^a   Ishimoto, Kiyoe ^a   Noda, Yusaku ^a   Sato, Yutaka ^a  

^a NAGOYA UNIVERSITY   (Japan)

Author keywords

Histone modification; miRNA; Posttranscriptional gene silencing; RNA dependent DNA methylation; Transcriptional gene silencing

Indexed keywords

CYTOSINE; MICRORNA; MICRORNA 820; UNCLASSIFIED DRUG;

ARTICLE; CACTA TRANSPOSABLE ELEMENT; CHROMOSOME 7; CONTROLLED STUDY; DNA METHYLATION; EPIGENETICS; GENE EXPRESSION; GENE LOCUS; GENETIC TRANSCRIPTION; HISTONE MODIFICATION; NONHUMAN; PLANT CHROMOSOME; TRANSPOSON;

BASE SEQUENCE; CHROMATIN IMMUNOPRECIPITATION; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; EPIGENOMICS; GENE SILENCING; HISTONES; MICRORNAS; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; POLYMERASE CHAIN REACTION; RNA, PLANT; RNA, SMALL INTERFERING; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EUKARYOTA;

EID: 84879997175     PISSN: 13417568     EISSN: 18805779     Source Type: Journal    
DOI: 10.1266/ggs.88.105     Document Type: Article

References (27)

1. Almeida, R., and Allshire, R. C. (2005) RNA silencing and genome regulation. Trends Cell Biol. 15, 251-258.
2. Ambros, V., Bartel, B., Bartel, D. P., Burge, C. B., Carrington, J. C., Chen, X. M., Dreyfuss, G., Eddy, S. R., Griffiths-Jones, S., Marshall, M., et al. (2003) A uniform system for microRNA annotation. RNA 9, 277-279.
3. Aravin, A. A., Hannon, G. J., and Brennecke, J. (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318, 761-764.
4. Cao, X. F., and Jacobsen, S. E. (2002) Role of the ArabidopsisDRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 12, 1138-1144.
5. Cao, X. F., Springer, N. M., Muszynski, M. G., Phillips, R. L., Kaeppler, S., and Jacobsen, S. E. (2000) Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc. Natl. Acad. Sci. USA 97, 4979-4984.
6. Carthew, R. W., and Sontheimer, E. J. (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642-655.
7. Chellappan, P., Xia, J., Zhou, X., Gao, S., Zhang, X., Coutino, G., Vazquez, F., Zhang, W., and Jin, H. (2010) siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res. 38, 6883-6894.
8. Feschotte, C., Jiang, N., and Wessler, S. R. (2002) Plant transposable elements: Where genetics meets genomics. Nat. Rev. Genet. 3, 329-341.
9. Henderson, I. R., Deleris, A., Wong, W., Zhong, X., Chin, H. G., Horwitz, G. A., Kelly, K. A., Pradhan, S., and Jacobsen, S. E. (2010) The de novo cytosine methyltransferase DRM2 requires intact UBA domains and a catalytically mutated paralog DRM3 during RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genet. 6, e1001182.
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. Kurihara, Y., Takashi, Y., and Watanabe, Y. (2006) The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 12, 206-212.
12. Lee, Y., Kim, M., Han, J. 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.
13. Lisch, D. (2009) Epigenetic regulation of transposable elements in plants. Annu. Rev. Plant Biol. 60, 43-66.
14. Matzke, M., Kanno, T., Daxinger, L., Huettel, B., and Matzke, A. J. M. (2009) RNA-mediated chromatin-based silencing in plants. Curr. Opin. Cell Biol. 21, 367-376.
15. Meyers, B. C., Axtell, M. J., Bartel, B., Bartel, D. P., Baulcombe, D., Bowman, J. L., Cao, X., Carrington, J. C., Chen, X., Green, P. J., et al. (2008) Criteria for annotation of plant microRNAs. Plant Cell 20, 3186-3190.
16. Miura, K., Agetsuma, M., Kitano, H., Yoshimura, A., Matsuoka, M., Jacobsen, S. E., and Ashikari, M. (2009) A metastable DWARF1 epigenetic mutant affecting plant stature in rice. Proc. Natl. Acad. Sci. USA 106, 11218-11223.
17. Nagaki, K., Cheng, Z. K., Ouyang, S., Talbert, P. B., Kim, M., Jones, K. M., Henikoff, S., Buell, C. R., and Jiang, J. M. (2004) Sequencing of a rice centromere uncovers active genes. Nat. Genet. 36, 138-145.
18. Nosaka, M., Itoh, J.-I., Nagato, Y., Ono, A., Ishiwata, A., and Sato, Y. (2012) Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice. PLoS Genet. 8, e1002953.
19. Plasterk, R. H. A. (2002) RNA silencing: The genome's immune system. Science 296, 1263-1265.
20. Sharma, R., Singh, R. K. M., Malik, G., Deveshwar, P., Tyagi, A. K., Kapoor, S., and Kapoor, M. (2009) Rice cytosine DNA methyltransferases-gene expression profiling during reproductive development and abiotic stress. FEBS J. 276, 6301-6311.
21. Sun, G. (2012) MicroRNAs and their diverse functions in plants. Plant Mol. Biol. 80, 17-36.
22. Vazquez, F., Blevins, T., Ailhas, J., Boller, T., and Meins, F., Jr. (2008) Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res. 36, 6429-6438.
23. Voinnet, O. (2008) Use, tolerance and avoidance of amplified RNA silencing by plants. Trends Plant Sci. 13, 317-328.
24. Voinnet, O. (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136, 669-687.
25. Wierzbicki, A. T. (2012) The role of long non-coding RNA in transcriptional gene silencing. Curr. Opin. Plant Biol. 15, 517-522.
26. Wu, L., Zhou, H., Zhang, Q., Zhang, J., Ni, F., Liu, C., and Qi, Y. (2010) DNA methylation mediated by a microRNA pathway. Mol. Cell 38, 465-475.
27. Zilberman, D., and Henikoff, S. (2004) Silencing of transposons in plant genomes: kick them when they're down. Genome Biol. 5, 249.