RNA decoys: An emerging component of plant regulatory networks?

Plant Signaling and Behavior

Volumn 7, Issue 9, 2012, Pages 1188-1193

  Banks, Isaac R ^a   Zhang, Yuanji ^a   Elizabeth Wiggins, B ^a   Heck, Greg R ^a   Ivashuta, Sergey ^a  

^a MONSANTO COMPANY   (United States)

Author keywords

Decoy; Gene regulation; MiR156; MiR160; MiR171; MiR172; MiR319; MiRNA; Soybean; Target mimicry

Indexed keywords

MICRORNA; PLANT RNA; TRANSCRIPTOME; UNTRANSLATED RNA;

ARABIDOPSIS; ARTICLE; BINDING SITE; CROP; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC ENGINEERING; GENETICS; SEQUENCE HOMOLOGY; TOBACCO;

ARABIDOPSIS; BINDING SITES; CROPS, AGRICULTURAL; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; GENETIC ENGINEERING; MICRORNAS; RNA, PLANT; RNA, UNTRANSLATED; SEQUENCE HOMOLOGY; TOBACCO; TRANSCRIPTOME;

ARABIDOPSIS THALIANA; EUKARYOTA; GLYCINE MAX; NICOTIANA BENTHAMIANA;

EID: 84866464613     PISSN: 15592316     EISSN: 15592324     Source Type: Journal    
DOI: 10.4161/psb.21299     Document Type: Article

References (36)

1. Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 2006; 57:19-53; PMID:16669754; http://dx.doi.org/10.1146/annurev.arplant.57.032905.105218
2. Shukla LI, Chinnusamy V, Sunkar R. The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochim Biophys Acta 2008; 1779:743-8
3. Carrington JC, Ambros V. Role of microRNAs in plant and animal development. Science 2003; 301:336-8; PMID:12869753; http://dx.doi.org/10.1126/science.1085242
4. Llave C, Xie Z, Kasschau KD, Carrington JC. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002; 297:2053-6; PMID:12242443; http://dx.doi.org/10.1126/science.1076311
5. Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, et al. Widespread translational inhibition by plant miRNAs and siRNAs. Science 2008; 320:1185-90; PMID:18483398; http://dx.doi.org/10.1126/science.1159151
6. Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, Reski R, et al. Transcriptional control of gene expression by microRNAs. Cell 2010; 140:111-22; PMID:20085706; http://dx.doi.org/10.1016/j.cell.2009.12.023
7. Chellappan P, Xia J, Zhou X, Gao S, Zhang X, Coutino G, et al. siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res 2010; 38:6883-94; PMID:20621980; http://dx.doi.org/10.1093/nar/gkq590
8. Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, et al. DNA methylation mediated by a microRNA pathway. Mol Cell 2010; 38:465-75; PMID:20381393; http://dx.doi.org/10.1016/j.molcel.2010.03.008
9. Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005; 121:207-21; PMID:15851028; http://dx.doi.org/10.1016/j.cell.2005.04.004
10. Wu G, Park MY, Conway SR, Wang JW, Weigel D, Poethig RS. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 2009; 138:750-9; PMID:19703400; http://dx.doi.org/10.1016/j.cell.2009.06.031
11. Bartel DP, Chen CZ. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet 2004; 5:396-400; PMID:15143321; http://dx.doi.org/10.1038/nrg1328
12. Hunter C, Willmann MR, Wu G, Yoshikawa M, de la Luz Gutiérrez-Nava M, Poethig SR. Trans-actingsiRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis. Development 2006; 133:2973-81; PMID:16818444; http://dx.doi.org/10.1242/dev.02491
13. Mallory AC, Bartel DP, Bartel B. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSEFACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 2005; 17:1360-75; PMID:15829600; http://dx.doi.org/10.1105/tpc.105.031716
14. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, et al. Control of leaf morphogenesis by microRNAs. Nature 2003; 425:257-63; PMID:12931144; http://dx.doi.org/10.1038/nature01958
15. Ivashuta S, Banks IR, Wiggins BE, Zhang Y, Ziegler TE, Roberts JK, et al. Regulation of gene expression in plants through miRNA inactivation. PLoS One 2011; 6:e21330; PMID:21731706; http://dx.doi.org/10.1371/journal.pone.0021330
16. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004; 23:4051-60; PMID:15372072; http://dx.doi.org/10.1038/sj.emboj.7600385
17. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants. Genes Dev 2002; 16:1616-26; PMID:12101121; http://dx.doi.org/10.1101/gad.1004402
18. Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009; 136:669-87; PMID:19239888; http://dx.doi.org/10.1016/j.cell.2009.01.046
19. Ramachandran V, Chen X. Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 2008; 321:1490-2; PMID:18787168; http://dx.doi.org/10.1126/science.1163728
20. Kai ZS, Pasquinelli AE. MicroRNA assassins: factors that regulate the disappearance of miRNAs. NatStruct Mol Biol 2010; 17:5-10; PMID:20051982; http://dx.doi.org/10.1038/nsmb.1762
21. Yan J, Gu Y, Jia X, Kang W, Pan S, Tang X, et al. Effective small RNA destruction by the expressionof a short tandem target mimic in Arabidopsis. Plant Cell 2012; 24:415-27; PMID:22345490; http://dx.doi.org/10.1105/tpc.111.094144
22. Lee Y, Jeon K, Lee JT, Kim S, Kim VN. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 2002; 21:4663-70; PMID:12198168; http://dx.doi.org/10.1093/emboj/cdf476
23. Kidner CA, Martienssen RA. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 2004; 428:81-4; PMID:14999284; http://dx.doi.org/10.1038/nature02366
24. Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, et al. Target mim-icry provides a new mechanism for regulation of microRNA activity. Nat Genet 2007; 39:1033-7; PMID:17643101; http://dx.doi.org/10.1038/ng2079
25. Todesco M, Rubio-Somoza I, Paz-Ares J, Weigel D. A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana. PLoS Genet 2010; 6:e1001031; PMID:20661442; http://dx.doi.org/10.1371/journal.pgen.1001031
26. Rymarquis LA, Kastenmayer JP, Hüttenhofer AG, Green PJ. Diamonds in the rough: mRNA-like non-coding RNAs. Trends Plant Sci 2008; 13:329-34; PMID:18448381; http://dx.doi.org/10.1016/j.tplants.2008.02.009
27. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP. Prediction of plant microRNA targets. Cell 2002; 110:513-20; PMID:12202040; http://dx.doi.org/10.1016/S0092-8674(02)00863-2
28. Aukerman MJ, Sakai H. Regulation of flowering time and floral organ identity by a MicroRNAand its APETALA2-like target genes. Plant Cell 2003; 15:2730-41; PMID:14555699; http://dx.doi.org/10.1105/tpc.016238
29. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004; 303:2022-5; PMID:12893888; http://dx.doi.org/10.1126/science.1088060
30. Schmid M, Uhlenhaut NH, Godard F, Demar M, Bressan R, Weigel D, et al. Dissection of floralinduction pathways using global expression analysis. Development 2003; 30:6001-12; PMID:14573523; http://dx.doi.org/10.1242/dev.00842
31. Wu G, Poethig RS. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 2006; 133:3539-47; PMID:16914499; http://dx.doi.org/10.1242/dev.02521
32. Cuperus JT, Fahlgren N, Carrington JC. Evolution and functional diversification of MIRNA genes. Plant Cell 2011; 23:431-42; PMID:21317375; http://dx.doi.org/10.1105/tpc.110.082784
33. Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 2011; 146:353-8; PMID:21802130; http://dx.doi.org/10.1016/j.cell.2011.07.014
34. Rubio-Somoza I, Weigel D, Franco-Zorilla JM, García JA, Paz-Ares J. ceRNAs: miRNA target mimic mimics. Cell 2011; 147:1431-2; PMID:22196719; http://dx.doi.org/10.1016/j.cell.2011.12.003
35. Ebert MS, Neilson JR, Sharp PA. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 2007; 4:721-6; PMID:17694064; http://dx.doi.org/10.1038/nmeth1079
36. Chatterjee S, Grosshans H. Active turnover modulates mature microRNA activity in Caenorhabditis elegans. Nature 2009; 461:546-9; PMID:19734881; http://dx.doi.org/10.1038/nature08349