Identification of 20 microRNAs from Oryza sativa.

MicroRNAs (miRNAs) are present in both plant and animal kingdoms and represents a growing family of non-coding RNAs. These tiny RNAs act as small guides and direct negative regulations usually in the process of development through sequence complementarity to target mRNAs. Although a large number of miRNAs have been identified from various animals, so far plant miRNA studies have focused mainly on Arabidopsis. Here we describe the identification of 20 miRNAs from a rice cDNA library. All the miRNAs were presumably processed from precursors with stem-loop structures and were positively detected in rice cells from at least one tissue, some of which showed tissue-specific expression. Twenty-three unique rice genes were identified to be feasible targets for seven rice miRNAs, including four members of Scarecrow-like transcription factor, the targets of miR-39 that had been characterized in Arabidopsis. Lacking long complementarity, the regulatory targets of 13 miRNAs remain to be further investigated. A possible mechanism of translational repressor for plant miRNAs that lack perfect complementarity to target mRNAs is discussed.

[1]  M. A. Rector,et al.  Endogenous and Silencing-Associated Small RNAs in Plants Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.003210. , 2002, The Plant Cell Online.

[2]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[3]  E. Lai.  Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation , 2002, Nature Genetics.

[4]  Jürgen Brosius,et al.  Experimental RNomics Identification of 140 Candidates for Small Non-Messenger RNAs in the Plant Arabidopsis thaliana , 2002, Current Biology.

[5]  G. Ruvkun,et al.  A uniform system for microRNA annotation. , 2003, RNA.

[6]  Liang-Hu Qu,et al.  The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa. , 2003, Nucleic acids research.

[7]  G. Hutvagner,et al.  A microRNA in a Multiple-Turnover RNAi Enzyme Complex , 2002, Science.

[8]  Hui Zhou,et al.  The Schizosaccharomyces pombe mgU6-47 gene is required for 2'-O-methylation of U6 snRNA at A41. , 2002, Nucleic acids research.

[9]  P. Chomczyński,et al.  Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. , 1987, Analytical biochemistry.

[10]  B. Cullen,et al.  MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[11]  A. Pasquinelli,et al.  Genes and Mechanisms Related to RNA Interference Regulate Expression of the Small Temporal RNAs that Control C. elegans Developmental Timing , 2001, Cell.

[12]  C. Napoli,et al.  Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans. , 1990, The Plant cell.

[13]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[14]  Hajime Sakai,et al.  Regulation of Flowering Time and Floral Organ Identity by a MicroRNA and Its APETALA2-Like Target Genes Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.016238. , 2003, The Plant Cell Online.

[15]  B. Reinhart,et al.  Prediction of Plant MicroRNA Targets , 2002, Cell.

[16]  L. Lim,et al.  An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans , 2001, Science.

[17]  J. Messing,et al.  CARPEL FACTORY, a Dicer Homolog, and HEN1, a Novel Protein, Act in microRNA Metabolism in Arabidopsis thaliana , 2002, Current Biology.

[18]  Bryan R. Cullen,et al.  RNA interference: antiviral defense and genetic tool , 2002, Nature Immunology.

[19]  C. Burge,et al.  Vertebrate MicroRNA Genes , 2003, Science.

[20]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[21]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[22]  David P. Bartel,et al.  MicroRNAs: At the Root of Plant Development?1 , 2003, Plant Physiology.

[23]  A. Hüttenhofer,et al.  RNomics: an experimental approach that identifies 201 candidates for novel, small, non‐messenger RNAs in mouse , 2001, The EMBO journal.

[24]  B. Reinhart,et al.  MicroRNAs in plants. , 2002, Genes & development.

[25]  K. Taira,et al.  Hes1 is a target of microRNA-23 during retinoic-acid-induced neuronal differentiation of NT2 cells , 2003, Nature.

[26]  C. Llave,et al.  Cleavage of Scarecrow-like mRNA Targets Directed by a Class of Arabidopsis miRNA , 2002, Science.

[27]  V. Ambros,et al.  Role of MicroRNAs in Plant and Animal Development , 2003, Science.

[28]  B. Samuelsson,et al.  Ribonuclease activity and RNA binding of recombinant human Dicer , 2002, The EMBO journal.

[29]  M. Mann,et al.  miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. , 2002, Genes & development.

[30]  Javier F. Palatnik,et al.  Control of leaf morphogenesis by microRNAs , 2003, Nature.

[31]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[32]  B. Reinhart,et al.  The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans , 2000, Nature.

[33]  G. Church,et al.  Computational and experimental identification of C. elegans microRNAs. , 2003, Molecular cell.

[34]  Richard A. Jorgensen,et al.  Chalcone synthase cosuppression phenotypes in petunia flowers: comparison of sense vs. antisense constructs and single-copy vs. complex T-DNA sequences , 1996, Plant Molecular Biology.

[35]  P. Benfey.  Molecular biology: MicroRNA is here to stay , 2003, Nature.

[36]  T. Tuschl,et al.  RNA interference is mediated by 21- and 22-nucleotide RNAs. , 2001, Genes & development.

[37]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[38]  Z. Xie,et al.  Negative Feedback Regulation of Dicer-Like1 in Arabidopsis by microRNA-Guided mRNA Degradation , 2003, Current Biology.

[39]  T. Tuschl,et al.  Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.

[40]  T. Tuschl,et al.  Identification of Tissue-Specific MicroRNAs from Mouse , 2002, Current Biology.

[41]  D. Marks,et al.  The small RNA profile during Drosophila melanogaster development. , 2003, Developmental cell.

[42]  V. Ambros,et al.  An Extensive Class of Small RNAs in Caenorhabditis elegans , 2001, Science.