Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana (original) (raw)
Bartel, D. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell116, 281–297 (2004). ArticleCAS Google Scholar
Ketting, R.F. et al. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev.15, 2654–2659 (2001). ArticleCAS Google Scholar
Hutvagner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science293, 834–838 (2001). ArticleCAS Google Scholar
Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature425, 415–419 (2003). ArticleCAS Google Scholar
Park, W., Li, J., Song, R., Messing, J. & Chen, X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana . Curr. Biol.12, 1484–1495 (2002). ArticleCAS Google Scholar
Kurihara, Y. & Watanabe, Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. USA101, 12753–12758 (2004). ArticleCAS Google Scholar
Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B. & Bartel, D.P. MicroRNAs in plants. Genes Dev.16, 1616–1626 (2002). ArticleCAS Google Scholar
Finnegan, E.J. & Matzke, M.A. The small RNA world. J. Cell Sci.116, 4689–4693 (2003). ArticleCAS Google Scholar
Floyd, S.K. & Bowman, J.L. Gene regulation: ancient microRNA target sequences in plants. Nature428, 485–486 (2004). ArticleCAS Google Scholar
Pasquinelli, A.E. et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature408, 86–89 (2000). ArticleCAS Google Scholar
Meyerowitz, E.M. Plants compared to animals: the broadest comparative study of development. Science295, 1482–1485 (2002). ArticleCAS Google Scholar
Jones-Rhoades, M.W. & Bartel, D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell14, 787–799 (2004). ArticleCAS Google Scholar
Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A. & Eddy, S.R. Rfam: an RNA family database. Nucleic Acids Res.31, 439–441 (2003). ArticleCAS Google Scholar
Palatnik, J.F. et al. Control of leaf morphogenesis by microRNAs. Nature425, 257–263 (2003). ArticleCAS Google Scholar
Aukerman, M.J. & Sakai, H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell15, 2730–2741 (2003). ArticleCAS Google Scholar
Chen, X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science303, 2022–2025 (2004). ArticleCAS Google Scholar
Mallory, A.C., Dugas, D.V., Bartel, D.P. & Bartel, B. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr. Biol.14, 1035–106 (2004). ArticleCAS Google Scholar
Achard, P., Herr, A., Baulcombe, D.C. & Harberd, N.P. Modulation of floral development by a gibberellin-regulated microRNA. Development131, 3357–3365 (2004). ArticleCAS Google Scholar
Emery, J.F. et al. Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes. Curr. Biol.13, 1768–1774 (2003). ArticleCAS Google Scholar
Laufs, P., Peaucelle, A., Morin, H. & Traas, J. MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development131, 4311–4322 (2004). ArticleCAS Google Scholar
Sunkar, R. & Zhu, J.K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis . Plant Cell16, 2001–2019 (2004). ArticleCAS Google Scholar
Xie, Z., Kasschau, K.D. & Carrington, J.C. Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr. Biol.13, 784–789 (2003). ArticleCAS Google Scholar
Vaucheret, H., Vazquez, F., Crete, P. & Bartel, D.P. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev.18, 1187–117 (2004). ArticleCAS Google Scholar
Levine, M. & Tjian, R. Transcription regulation and animal diversity. Nature424, 147–151 (2003). ArticleCAS Google Scholar
Teichmann, S.A. & Babu, M.M. Gene regulatory network growth by duplication. Nat. Genet.36, 492–496 (2004). ArticleCAS Google Scholar
Rhoades, M.W. et al. Prediction of plant microRNA targets. Cell110, 513–520 (2002). ArticleCAS Google Scholar
Vazquez, F., Gasciolli, V., Crete, P. & Vaucheret, H. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol.14, 346–351 (2004). ArticleCAS Google Scholar
Dunoyer, P., Lecellier, C.H., Parizotto, E.A., Himber, C. & Voinnet, O. Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing. Plant Cell16, 1235–1250 (2004). ArticleCAS Google Scholar
Llave, C., Kasschau, K.D., Rector, M.A. & Carrington, J.C. Endogenous and silencing-associated small RNAs in plants. Plant Cell14, 1605–1619 (2002). ArticleCAS Google Scholar
Papp, I. et al. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol.132, 1382–1390 (2003). ArticleCAS Google Scholar
Xie, Z. et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol.2, E104 (2004). Article Google Scholar
Peragine, A., Yoshikawa, M., Wu, G., Albrecht, H.L. & Poethig, R.S. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis . Genes Dev.18, 2368–2379 (2004). ArticleCAS Google Scholar
Vazquez, F. et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell16, 69–79 (2004). ArticleCAS Google Scholar
Schauer, S.E., Jacobsen, S.E., Meinke, D.W. & Ray, A. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci.7, 487–491 (2002). ArticleCAS Google Scholar
Holder, M. & Lewis, P.O. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet.4, 275–284 (2003). ArticleCAS Google Scholar
Mallory, A.C. et al. MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region. EMBO J.23, 3356–3364 (2004). ArticleCAS Google Scholar
Kasschau, K.D. et al. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev. Cell4, 205–217 (2003). ArticleCAS Google Scholar
Bartel, B. & Bartel, D.P. MicroRNAs: at the root of plant development? Plant Physiol.132, 709–717 (2003). ArticleCAS Google Scholar
Llave, C., Xie, Z., Kasschau, K.D. & Carrington, J.C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science297, 2053–2056 (2002). ArticleCAS Google Scholar
Herbert, A. The four Rs of RNA-directed evolution. Nat. Genet.36, 19–25 (2004). ArticleCAS Google Scholar
Bartel, D.P. & Chen, C.Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet.5, 396–400 (2004). ArticleCAS Google Scholar
Hurles, M. Gene duplication: the genomic trade in spare parts. PLoS Biol.2, E206 (2004). Article Google Scholar
Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet.16, 276–277 (2000). ArticleCAS Google Scholar
Lin, J.-T. Alternatives to Hamaker's approximations to the cumulative normal distribution and its inverse. Statistician37, 413–414 (1988). Article Google Scholar
Notredame, C., Higgins, D.G. & Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol.302, 205–217 (2000). ArticleCAS Google Scholar
Huelsenbeck, J.P. & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics17, 754–755 (2001). ArticleCAS Google Scholar
Posada, D. & Crandall, K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics14, 817–818 (1998). ArticleCAS Google Scholar
Swofford, D PAUP*: Phylogenetic analysis using parsimony (*and other methods) 4.0b10 edn. (Sinauer, Sunderland, Massachusetts, 2002). Google Scholar