It's a Small RNA World, After All

Small RNAs (sRNAs) can regulate transcript and protein abundance. Previously, they have been identified using traditional cloning approaches, which has limited how many could be characterized. Now, the Meyers and Green laboratories have used massively parallel signature sequencing technology to find over 1.5 million sRNAs in Arabidopsis thaliana. These new sRNAs reveal a greater-than-expected potential role for sRNAs in gene regulation, preferential expression or usage of sRNAs in flowers, and the prospect of targeted sRNA-mediated regulation of pseudogenes. In addition, new plant microRNAs have been identified, some of which may be unique to Arabidopsis.

[1]  Phillip D. Zamore,et al.  Ribo-gnome: The Big World of Small RNAs , 2005, Science.

[2]  O. Mathieu,et al.  RNA-directed DNA methylation , 2004, Journal of Cell Science.

[3]  C. Alonso.  Nonsense-mediated RNA decay: a molecular system micromanaging individual gene activities and suppressing genomic noise. , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

[4]  S. Henikoff,et al.  DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes , 2005, Current Biology.

[5]  Yeonhee Choi,et al.  One-Way Control of FWA Imprinting in Arabidopsis Endosperm by DNA Methylation , 2004, Science.

[6]  Scott A. Givan,et al.  ASRP: the Arabidopsis Small RNA Project Database , 2004, Nucleic Acids Res..

[7]  Guiliang Tang,et al.  Biochemical dissection of RNA silencing in plants. , 2004, Methods in molecular biology.

[8]  Joseph M. Dale,et al.  Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome , 2003, Science.

[9]  James A. Birchler,et al.  RNAi-mediated pathways in the nucleus , 2005, Nature Reviews Genetics.

[10]  Todd Blevins,et al.  RNA silencing systems and their relevance to plant development. , 2005, Annual review of cell and developmental biology.

[11]  Blake C Meyers,et al.  The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. , 2004, Genome research.

[12]  Adam M. Gustafson,et al.  microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants , 2005, Cell.

[13]  R. Martienssen,et al.  The role of RNA interference in heterochromatic silencing , 2004, Nature.

[14]  Michael Black,et al.  Role of transposable elements in heterochromatin and epigenetic control , 2004, Nature.

[15]  David C. Baulcombe,et al.  RNA silencing. , 2005, Trends in biochemical sciences.

[16]  J. Bennetzen,et al.  The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences. , 2002, Genetics.

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

[18]  Shivakundan Singh Tej,et al.  Elucidation of the Small RNA Component of the Transcriptome , 2005, Science.

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

[20]  L. Maquat,et al.  An enemy within: fly reconnaissance deploys an endonuclease to destroy nonsense-containing mRNA. , 2004, Trends in cell biology.