The small RNA world

Small RNAs have burst on the scene as ubiquitous, versatile repressors of gene expression in plants, animals and many fungi. These tiny RNAs (∼21-26 nt), which induce silencing through homologous sequence interactions, come in many guises: short interfering (si) RNAs ([Elbashir et al., 2001][1]),

[1]  Xiaodong Wang,et al.  R2D2, a Bridge Between the Initiation and Effector Steps of the Drosophila RNAi Pathway , 2003, Science.

[2]  V. Ambros,et al.  MicroRNAs and Other Tiny Endogenous RNAs in C. elegans , 2003, Current Biology.

[3]  M. Carmell,et al.  Posttranscriptional Gene Silencing in Plants , 2006 .

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

[5]  W. Filipowicz,et al.  Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Christophe Antoniewski,et al.  Absence of transitive and systemic pathways allows cell-specific and isoform-specific RNAi in Drosophila. , 2003, RNA.

[7]  Christophe Ritzenthaler,et al.  Transitivity‐dependent and ‐independent cell‐to‐cell movement of RNA silencing , 2003, The EMBO journal.

[8]  A. Pasquinelli,et al.  A Cellular Function for the RNA-Interference Enzyme Dicer in the Maturation of the let-7 Small Temporal RNA , 2001, Science.

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

[10]  F. Slack,et al.  The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. , 2003, Developmental biology.

[11]  F. Slack,et al.  Control of developmental timing by small temporal RNAs: a paradigm for RNA‐mediated regulation of gene expression , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

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

[13]  J. P. Jackson,et al.  Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase , 2002, Nature.

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

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

[16]  A. Fire,et al.  Specific interference by ingested dsRNA , 1998, Nature.

[17]  Kenneth Y. Tsai,et al.  Control of CpNpG DNA methylation by the KRYPTONITE histone H 3 methyltransferase , 2002 .

[18]  D. Sahagian,et al.  El Niño Events Recorded by Stalagmite Carbon Isotopes , 2002, Science.

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

[20]  R. Allshire,et al.  Hairpin RNAs and Retrotransposon LTRs Effect RNAi and Chromatin-Based Gene Silencing , 2003, Science.

[21]  Raul Andino,et al.  Nucleic Acid-Based Immune System: the Antiviral Potential of Mammalian RNA Silencing , 2003, Journal of Virology.

[22]  Olivier Voinnet,et al.  RNA silencing: small RNAs as ubiquitous regulators of gene expression. , 2002, Current opinion in plant biology.

[23]  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.

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

[25]  S. Ding,et al.  Induction and Suppression of RNA Silencing by an Animal Virus , 2002, Science.

[26]  A. Rougvie,et al.  The Caenorhabditis elegans hunchback-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. , 2003, Developmental cell.

[27]  P. Waterhouse,et al.  Posttranscriptional Gene Silencing Is Not Compromised in the Arabidopsis CARPEL FACTORY (DICER-LIKE1) Mutant, a Homolog of Dicer-1 from Drosophila , 2003, Current Biology.

[28]  M. Yao,et al.  Programmed DNA Deletion As an RNA-Guided System of Genome Defense , 2003, Science.

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

[30]  Ira M. Hall,et al.  Establishment and Maintenance of a Heterochromatin Domain , 2002, Science.

[31]  Michael Q. Zhang,et al.  The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. , 2002, Genes & development.

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

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

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

[35]  V. Ambros,et al.  The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. , 1999, Developmental biology.

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

[37]  Ira M. Hall,et al.  RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast , 2002, Proceedings of the National Academy of Sciences of the United States of America.

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

[39]  H. Vaucheret,et al.  RNA Silencing and the Mobile Silencing Signal Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.001677. , 2002, The Plant Cell Online.

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

[41]  Craig P. Hunter,et al.  Systemic RNAi in C. elegans Requires the Putative Transmembrane Protein SID-1 , 2002, Science.

[42]  Chiara Gamberi,et al.  The C elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. , 2003, Developmental cell.

[43]  O. Voinnet RNA silencing bridging the gaps in wheat extracts. , 2003, Trends in plant science.

[44]  B. Reinhart,et al.  Small RNAs Correspond to Centromere Heterochromatic Repeats , 2002, Science.

[45]  K. D. Kasschau,et al.  A MicroRNA as a Translational Repressor of APETALA 2 in Arabidopsis Flower Development , 2022 .

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

[47]  J. Birchler,et al.  RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. , 2002, Molecular cell.

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

[49]  V. Kim,et al.  MicroRNA maturation: stepwise processing and subcellular localization , 2002, The EMBO journal.

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

[51]  E. H. Feinberg,et al.  Transport of dsRNA into Cells by the Transmembrane Protein SID-1 , 2003, Science.

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

[53]  R. Russell,et al.  bantam Encodes a Developmentally Regulated microRNA that Controls Cell Proliferation and Regulates the Proapoptotic Gene hid in Drosophila , 2003, Cell.

[54]  C. Cogoni,et al.  RNA-mediated gene silencing , 2003, Cellular and Molecular Life Sciences CMLS.

[55]  H. Vaucheret,et al.  Systemic acquired silencing: transgene‐specific post‐transcriptional silencing is transmitted by grafting from silenced stocks to non‐silenced scions , 1997, The EMBO journal.

[56]  Animesh Ray,et al.  DICER-LIKE1: blind men and elephants in Arabidopsis development. , 2002, Trends in plant science.

[57]  B. Reinhart,et al.  A viral suppressor of RNA silencing differentially regulates the accumulation of short interfering RNAs and micro-RNAs in tobacco , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[58]  S. Hammond,et al.  An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells , 2000, Nature.

[59]  C. Rieder,et al.  Greatwall kinase , 2004, The Journal of cell biology.

[60]  Peter M. Waterhouse,et al.  Exploring plant genomes by RNA-induced gene silencing , 2003, Nature Reviews Genetics.

[61]  H. Vaucheret,et al.  RNA Silencing in Plants--Defense and Counterdefense , 2001, Science.

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

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

[64]  D. Baulcombe,et al.  Systemic Spread of Sequence-Specific Transgene RNA Degradation in Plants Is Initiated by Localized Introduction of Ectopic Promoterless DNA , 1998, Cell.

[65]  C. Burge,et al.  The microRNAs of Caenorhabditis elegans. , 2003, Genes & development.

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

[67]  A. Caudy,et al.  Role for a bidentate ribonuclease in the initiation step of RNA interference , 2001 .

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

[69]  S. Ishii,et al.  Generation of Ski-knockdown mice by expressing a long double-strand RNA from an RNA polymerase II promoter. , 2003, Genes & development.

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

[71]  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.

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

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

[74]  T. Fujisawa,et al.  Analysis of a piwi-Related Gene Implicates Small RNAs in Genome Rearrangement in Tetrahymena , 2002, Cell.

[75]  Marjori Matzke,et al.  Evidence for Nuclear Processing of Plant Micro RNA and Short Interfering RNA Precursors1[w] , 2003, Plant Physiology.

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

[77]  Phillip D Zamore,et al.  Ancient Pathways Programmed by Small RNAs , 2002, Science.

[78]  R. Poethig,et al.  miSSING LINKS: miRNAs and plant development. , 2003, Current opinion in genetics & development.

[79]  G. Hannon,et al.  RNAi: an ever-growing puzzle. , 2003, Trends in biochemical sciences.

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

[81]  T. Volpe,et al.  RNA interference is required for normal centromere function infission yeast , 2004, Chromosome Research.

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

[83]  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.

[84]  H. L. Sänger,et al.  RNA-directed de novo methylation of genomic sequences in plants , 1994, Cell.

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

[86]  B. Reinhart,et al.  Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA , 2000, Nature.

[87]  A. Pasquinelli,et al.  Control of developmental timing by micrornas and their targets. , 2002, Annual review of cell and developmental biology.

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