Micro RNAs and Short‐interfering RNAs in Plants

Gene silencing can occur either at the transcriptional level or post-transcriptional level or both. Many instances of sequence-specific silencing requires small RNAs that can be divided into two major classes: microRNAs (miRNAs) and short-interfering RNAs (siRNAs). miRNAs function in post-transcriptional gene silencing by guiding mRNA degradation or translational repression. Endogenous siRNAs are more diverse in plants than in animals and can direct post-transcriptional gene silencing through mRNA degradation or transcriptional gene silencing by trigger- ing DNA methylation and histone modifications. This review discusses recent advances in the field of small RNA- guided gene silencing in plants including rice.

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

[2]  Jian-Kang Zhu,et al.  A miRNA Involved in Phosphate-Starvation Response in Arabidopsis , 2005, Current Biology.

[3]  B. F. Vaniushin,et al.  [DNA methylation and epigenetics]. , 2006, Genetika.

[4]  P. Waterhouse,et al.  Role of short RNAs in gene silencing. , 2001, Trends in plant science.

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

[6]  H. Cerutti,et al.  Transgene and transposon silencing in Chlamydomonas reinhardtii by a DEAH-box RNA helicase. , 2000, Science.

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

[8]  D. Bartel,et al.  MicroRNAS and their regulatory roles in plants. , 2006, Annual review of plant biology.

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

[10]  Marjori Matzke,et al.  Genetic analysis of RNA-mediated transcriptional gene silencing. , 2004, Biochimica et biophysica acta.

[11]  H. Vaucheret,et al.  Functions of microRNAs and related small RNAs in plants , 2006, Nature Genetics.

[12]  Tamas Dalmay,et al.  An RNA-Dependent RNA Polymerase Gene in Arabidopsis Is Required for Posttranscriptional Gene Silencing Mediated by a Transgene but Not by a Virus , 2000, Cell.

[13]  Izabela Makalowska,et al.  Overlapping genes in vertebrate genomes , 2005, Comput. Biol. Chem..

[14]  P. Laufs,et al.  The Balance between the MIR164A and CUC2 Genes Controls Leaf Margin Serration in Arabidopsis[W] , 2006, The Plant Cell Online.

[15]  Adam M. Gustafson,et al.  Genetic and Functional Diversification of Small RNA Pathways in Plants , 2004, PLoS biology.

[16]  Nicolas Bouché,et al.  An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs , 2006, The EMBO journal.

[17]  Thomas Girke,et al.  Identification and characterization of endogenous small interfering RNAs from rice , 2005, Nucleic acids research.

[18]  M. Matzke,et al.  Transcriptional silencing and promoter methylation triggered by double‐stranded RNA , 2000, The EMBO journal.

[19]  B. Reinhart,et al.  A biochemical framework for RNA silencing in plants. , 2003, Genes & development.

[20]  E. K. Yoon,et al.  ‘Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells’ , 2006, Nucleic acids research.

[21]  Diana V. Dugas,et al.  MicroRNA Regulation of NAC-Domain Targets Is Required for Proper Formation and Separation of Adjacent Embryonic, Vegetative, and Floral Organs , 2004, Current Biology.

[22]  R. Poethig,et al.  A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. , 2005, Genes & development.

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

[24]  Yukihisa Shimada,et al.  GAMYB controls different sets of genes and is differentially regulated by microRNA in aleurone cells and anthers. , 2006, The Plant journal : for cell and molecular biology.

[25]  C. Pikaard,et al.  Plant Nuclear RNA Polymerase IV Mediates siRNA and DNA Methylation-Dependent Heterochromatin Formation , 2005, Cell.

[26]  Cathie Martin,et al.  SERRATE: a new player on the plant microRNA scene , 2006, EMBO reports.

[27]  Edwards Allen,et al.  DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[28]  D. Bartel,et al.  A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. , 2006, Genes & development.

[29]  Jonathan D. G. Jones,et al.  A Plant miRNA Contributes to Antibacterial Resistance by Repressing Auxin Signaling , 2006, Science.

[30]  Thomas Tuschl,et al.  Identification and characterization of small RNAs involved in RNA silencing , 2005, FEBS letters.

[31]  Elliot M. Meyerowitz,et al.  The early extra petals1 Mutant Uncovers a Role for MicroRNA miR164c in Regulating Petal Number in Arabidopsis , 2005, Current Biology.

[32]  Cameron Johnson,et al.  CSRDB: a small RNA integrated database and browser resource for cereals , 2006, Nucleic Acids Res..

[33]  David P. Bartel,et al.  Partially Redundant Functions of Arabidopsis DICER-like Enzymes and a Role for DCL4 in Producing trans-Acting siRNAs , 2005, Current Biology.

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

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

[36]  S. Lerbs-Mache,et al.  Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. , 2005, Genes & development.

[37]  D. Bartel,et al.  MicroRNA-Directed Regulation of Arabidopsis AUXIN RESPONSE FACTOR17 Is Essential for Proper Development and Modulates Expression of Early Auxin Response Genesw⃞ , 2005, The Plant Cell Online.

[38]  Michelle T. Juarez,et al.  microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity , 2004, Nature.

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

[40]  M. Pellegrini,et al.  Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis , 2006, Cell.

[41]  H. Vaucheret,et al.  Arabidopsis HEN1 A Genetic Link between Endogenous miRNA Controlling Development and siRNA Controlling Transgene Silencing and Virus Resistance , 2003, Current Biology.

[42]  A. Werner Natural Antisense Transcripts , 2005, RNA biology.

[43]  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.

[44]  D. Zilberman,et al.  RNA Silencing Genes Control de Novo DNA Methylation , 2004, Science.

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

[46]  F. Gubler,et al.  The Arabidopsis GAMYB-Like Genes, MYB33 and MYB65, Are MicroRNA-Regulated Genes That Redundantly Facilitate Anther Development , 2005, The Plant Cell Online.

[47]  Ronald H. A. Plasterk,et al.  RNA Silencing: The Genome's Immune System , 2002, Science.

[48]  A. Si-Ammour,et al.  Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing , 2006, Nucleic acids research.

[49]  J. Bowman,et al.  Radial Patterning of Arabidopsis Shoots by Class III HD-ZIP and KANADI Genes , 2003, Current Biology.

[50]  R. Plasterk,et al.  mut-7 of C. elegans, Required for Transposon Silencing and RNA Interference, Is a Homolog of Werner Syndrome Helicase and RNaseD , 1999, Cell.

[51]  Xiaofeng Cao,et al.  ARGONAUTE4 Control of Locus-Specific siRNA Accumulation and DNA and Histone Methylation , 2003, Science.

[52]  Xuemei Chen,et al.  A MicroRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development , 2004, Science.

[53]  Franck Vazquez,et al.  The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. , 2004, Genes & development.

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

[55]  Hai Huang,et al.  SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. , 2006, The Plant journal : for cell and molecular biology.

[56]  Terry Gaasterland,et al.  Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana , 2005, Genome Biology.

[57]  Xuemei Chen,et al.  Methylation as a Crucial Step in Plant microRNA Biogenesis , 2005, Science.

[58]  Gang Wu,et al.  Trans-acting siRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis , 2006, Development.

[59]  Hailing Jin,et al.  A pathogen-inducible endogenous siRNA in plant immunity , 2006, Proceedings of the National Academy of Sciences.

[60]  Yan Li,et al.  Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post‐embryogenic development , 2006, FEBS letters.

[61]  Gang Wu,et al.  Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3 , 2006, Development.

[62]  R. Sunkar,et al.  Posttranscriptional Induction of Two Cu/Zn Superoxide Dismutase Genes in Arabidopsis Is Mediated by Downregulation of miR398 and Important for Oxidative Stress Tolerance[W] , 2006, The Plant Cell Online.

[63]  Heinz Saedler,et al.  The miRNA156/157 recognition element in the 3' UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. , 2007, The Plant journal : for cell and molecular biology.

[64]  P. Jeffrey,et al.  Regulation of Heterochromatic Silencing and Histone H 3 Lysine-9 Methylation by RNAi , 2002 .

[65]  Gang Wu,et al.  SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. , 2004, Genes & development.

[66]  Ira M. Hall,et al.  Regulation of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation by RNAi , 2002, Science.

[67]  Rogerio Margis,et al.  The evolution and diversification of Dicers in plants , 2006, FEBS letters.

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

[69]  Edwards Allen,et al.  P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. , 2003, Developmental cell.

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

[71]  H. Lipkin Where is the ?c? , 1978 .

[72]  Ramanjulu Sunkar,et al.  Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. , 2007, Trends in plant science.

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

[74]  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.

[75]  M. Matzke,et al.  HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double‐stranded RNA , 2002, The EMBO journal.

[76]  G. Ruvkun,et al.  Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans , 1993, Cell.

[77]  C. Llave,et al.  P 1 / HC-Pro , a Viral Suppressor of RNA Silencing , Interferes with Arabidopsis Development and miRNA , 2003 .

[78]  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.

[79]  Andrew Fire,et al.  The rde-1 Gene, RNA Interference, and Transposon Silencing in C. elegans , 1999, Cell.

[80]  Patrick Laufs,et al.  MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems , 2004, Development.

[81]  Shivakundan Singh Tej,et al.  MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. , 2006, Genome research.

[82]  H. Vaucheret Post-transcriptional small RNA pathways in plants: mechanisms and regulations. , 2006, Genes & development.

[83]  Olivier Voinnet,et al.  Two classes of short interfering RNA in RNA silencing , 2002, The EMBO journal.

[84]  Chun-Lin Su,et al.  Regulation of Phosphate Homeostasis by MicroRNA in Arabidopsis[W] , 2005, The Plant Cell Online.

[85]  A. Berdal,et al.  Natural antisense transcripts: sound or silence? , 2005, Physiological Genomics.

[86]  N. Chua,et al.  MicroRNA Directs mRNA Cleavage of the Transcription Factor NAC1 to Downregulate Auxin Signals for Arabidopsis Lateral Root Development , 2005, The Plant Cell Online.

[87]  Olivier Voinnet,et al.  RNA silencing of host transcripts by cauliflower mosaic virus requires coordinated action of the four Arabidopsis Dicer-like proteins , 2006, Proceedings of the National Academy of Sciences.

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

[89]  D. Baulcombe,et al.  RNA Polymerase IV Directs Silencing of Endogenous DNA , 2005, Science.

[90]  E. Richards,et al.  The value-added genome: building and maintaining genomic cytosine methylation landscapes. , 2004, Current opinion in genetics & development.

[91]  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.

[92]  S. Jacobsen,et al.  The Arabidopsis Chromatin-Modifying Nuclear siRNA Pathway Involves a Nucleolar RNA Processing Center , 2006, Cell.

[93]  J. Carrington,et al.  Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA Affects Developmental Timing and Patterning in Arabidopsis , 2006, Current Biology.

[94]  O. Voinnet RNA silencing as a plant immune system against viruses. , 2001, Trends in genetics : TIG.

[95]  Nam-Hai Chua,et al.  ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. , 2007, The Plant journal : for cell and molecular biology.

[96]  Patrick Achard,et al.  Modulation of floral development by a gibberellin-regulated microRNA , 2004, Development.

[97]  Thomas Girke,et al.  Cloning and Characterization of MicroRNAs from Ricew⃞ , 2005, The Plant Cell Online.

[98]  L. Xiong,et al.  Genomic Organization, Differential Expression, and Interaction of SQUAMOSA Promoter-Binding-Like Transcription Factors and microRNA156 in Rice1[W] , 2006, Plant Physiology.

[99]  Songtao Jia,et al.  RNAi-Mediated Targeting of Heterochromatin by the RITS Complex , 2004, Science.

[100]  I. Henderson,et al.  RNAi, DRD1, and Histone Methylation Actively Target Developmentally Important Non-CG DNA Methylation in Arabidopsis , 2006, PLoS genetics.

[101]  Xiaofeng Cao,et al.  Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats , 2004, Current Biology.

[102]  Shoshi Kikuchi,et al.  Antisense transcripts with rice full-length cDNAs , 2003, Genome Biology.

[103]  Franck Vazquez,et al.  Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. , 2004, Molecular cell.

[104]  Philippe Mourrain,et al.  Arabidopsis SGS2 and SGS3 Genes Are Required for Posttranscriptional Gene Silencing and Natural Virus Resistance , 2000, Cell.

[105]  David P. Bartel,et al.  A Two-Hit Trigger for siRNA Biogenesis in Plants , 2006, Cell.

[106]  Phillip A Sharp,et al.  siRNAs can function as miRNAs , 2003 .

[107]  O. Borsani,et al.  Endogenous siRNAs Derived from a Pair of Natural cis-Antisense Transcripts Regulate Salt Tolerance in Arabidopsis , 2005, Cell.