Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post‐embryogenic development

In vitro cultured embryogenic callus was employed as a model to investigate microRNAs (miRNAs) associated with embryogenesis and post‐embryonic development. Thirty‐one miRNAs including 16 novel species were identified from a large number of small RNAs which were cloned from both differentiated and undifferentiated rice embryogenic calli. Four target genes of the miRNAs were further validated. A set of the miRNAs, including miR397 and miR156, exhibited intriguing expression patterns during the transition from undifferentiated to differentiated calli. By exploiting the correlations between the differential expression patterns of these miRNAs and their targets, the regulatory roles of the miRNAs on meristem maintenance and embryogenesis were indicated.

[1]  Hong Jiang,et al.  Identification of human fetal liver miRNAs by a novel method , 2005, FEBS letters.

[2]  A. Adai,et al.  Computational prediction of miRNAs in Arabidopsis thaliana. , 2005, Genome research.

[3]  C. P. Constabel,et al.  Polyphenol oxidase from hybrid poplar. Cloning and expression in response to wounding and herbivory. , 2000, Plant physiology.

[4]  David C Baulcombe,et al.  Cloning and characterization of micro-RNAs from moss. , 2005, The Plant journal : for cell and molecular biology.

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

[6]  R. Sunkar,et al.  Novel and Stress-Regulated MicroRNAs and Other Small RNAs from Arabidopsis , 2004, The Plant Cell Online.

[7]  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.

[8]  Vincent L. Chiang,et al.  Novel and Mechanical Stress–Responsive MicroRNAs in Populus trichocarpa That Are Absent from Arabidopsisw⃞ , 2005, The Plant Cell Online.

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

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

[11]  Marjori Matzke,et al.  Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation , 2003, Current Biology.

[12]  Yuanji Zhang,et al.  miRU: an automated plant miRNA target prediction server , 2005, Nucleic Acids Res..

[13]  Baohong Zhang,et al.  Conservation and divergence of plant microRNA genes. , 2006, The Plant journal : for cell and molecular biology.

[14]  P. Huijser,et al.  Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition. , 1997, The Plant journal : for cell and molecular biology.

[15]  P. Benfey,et al.  Signals that regulate stem cell activity during plant development. , 2005, Current opinion in genetics & development.

[16]  Anders Krogh,et al.  Computational evidence for hundreds of non-conserved plant microRNAs , 2005, BMC Genomics.

[17]  J. Zimmerman.  Somatic Embryogenesis: A Model for Early Development in Higher Plants. , 1993, The Plant cell.

[18]  Javier F. Palatnik,et al.  Specific effects of microRNAs on the plant transcriptome. , 2005, Developmental cell.

[19]  D. Bartel,et al.  Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. , 2004, Molecular cell.

[20]  Baohong Zhang,et al.  Identification of 188 conserved maize microRNAs and their targets , 2006, FEBS letters.

[21]  E. Selker,et al.  Controlling DNA methylation: many roads to one modification. , 2005, Current opinion in genetics & development.

[22]  S. Jayasena,et al.  Functional siRNAs and miRNAs Exhibit Strand Bias , 2003, Cell.

[23]  Liang-Hu Qu,et al.  Identification of 20 microRNAs from Oryza sativa. , 2004, Nucleic acids research.

[24]  T. Du,et al.  Asymmetry in the Assembly of the RNAi Enzyme Complex , 2003, Cell.

[25]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[26]  N. Chua,et al.  The WUSCHEL gene promotes vegetative-to-embryonic transition in Arabidopsis. , 2002, The Plant journal : for cell and molecular biology.

[27]  Terry Gaasterland,et al.  Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets , 2004, Genome Biology.

[28]  Bin Liu,et al.  Loss of Function of OsDCL1 Affects MicroRNA Accumulation and Causes Developmental Defects in Rice1[w] , 2005, Plant Physiology.

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

[30]  P. Rouzé,et al.  Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.