Institute of Information Science, Academia Sinica



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TIGP--Combining data-mining and experimental validation for the discovery of Arabidopsis small non-coding RNAs

  • LecturerDr. Shu-Hsing Wu (Institute of Plant and Microbial Biology, Academia Sinica)
    Host: Miss Elsa Pan
  • Time2010-10-28 (Thu.) 14:00 – 15:00
  • LocationAuditorium 106 at new IIS Building
Non-coding RNAs (ncRNAs) play vital roles in translation, splicing, RNA processing, RNA modification and regulation of gene expression. The advancement in ncRNA discovery is evolving along with the finding of new classes of ncRNAs and the invention of revolutionary sequencing platforms. High-throughput sequencing technologies greatly facilitate the study of small regulatory RNAs which are 20 to 30 nt in length. Those studies include the computational approaches which use small RNA sequencing data for the studies of ncRNAs. I will present the development of novel bioinformatics approaches to analyze small RNA sequencing data for the discovery of novel trans-acting small interfering RNAs (siRNA) in Arabidopsis. Also, the effect of RNA silencing in plants can be amplified if secondary small interfering RNA (siRNA) production is triggered by the interaction of microRNAs (miRNAs) or siRNAs with a long target RNA. However, miRNA and siRNA interactions are not all equivalent because most of them do not trigger secondary siRNA production. I will also show evidence that the secondary siRNA triggers are miRNAs and trans-acting siRNAs of 22 nt, rather than the more typical 21-nt length. The function of small RNAs is influenced by size and that the length 22 nt facilitates the triggering of secondary siRNA production. Our research demonstrates that, by combining pre-existing biological knowledge and appropriate mining approaches, small RNA sequencing data represent a wealth treasure for the studies of small regulatory RNAs. References Chen, H.M., Chen, L.T., Patel, K., Li, Y.H., Baulcombe, D.C., and Wu, S.H.* (2010). 22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci U S A 107, 15269-15274. Chen H.-M., Li Y.-H. and Wu S.-H* (2007) Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc. Natl. Acad. Sci. USA 104, 3318-3323