RNA Interference and Small Interfering RNAs

The term aRNA interferenceo (RNAi) was coined after the groundbreaking discovery that injection of double-stranded RNA (dsRNA) into the nematode Caenorhabditis elegans leads to specific silencing of genes highly homologous in sequence to the delivered dsRNA. The RNAi phenotype is either identical to the genetic null mutant or resembles an allelic series of mutants. The dsRNA can also be delivered by feeding bacteria that express dsRNA from recombinant plasmids to the worm or by soaking the worm in a solution containing the dsRNA. 3] In rapid sequence, RNAi was observed in other animals including mice, 5] and therefore this process possibly exists also in humans. RNAi appears to be related to the posttranscriptional gene silencing (PTGS) mechanism of cosuppression in plants and quelling in fungi. Cosuppression is the ability of some transgenes to silence both themselves and homologous chromosomal loci simultaneously. The initiator molecule for cosuppression is believed to be aberrant RNA, possibly dsRNA, and some components of the RNAi machinery are required for posttranscriptional silencing by cosuppression. 8, 13] The natural function of RNAi and cosuppression is thought to be protection of the genome against invasion by mobile genetic elements such as transposons and viruses, which produce aberrant RNA or dsRNA in the host cell when they become active. Thus, specific mRNA degradation is thought to prevent transposon and virus replication. This minireview will highlight recent advances in understanding the molecular mechanism of RNAi and its biological function. The reader is also referred to a number of excellent reviews that have appeared recently (see refs. [18 ± 24]).

[1]  Magdalena Zernicka-Goetz,et al.  Specific interference with gene function by double-stranded RNA in early mouse development , 2000, Nature Cell Biology.

[2]  B. Williams,et al.  Identification of genes differentially regulated by interferon α, β, or γ using oligonucleotide arrays , 1998 .

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

[4]  A. Sánchez Alvarado,et al.  Double-stranded RNA specifically disrupts gene expression during planarian regeneration. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[5]  K. Kasschau,et al.  A Counterdefensive Strategy of Plant Viruses Suppression of Posttranscriptional Gene Silencing , 1998, Cell.

[6]  S. Balzergue,et al.  Activation of systemic acquired silencing by localised introduction of DNA , 1999, Current Biology.

[7]  Ronald H. A. Plasterk,et al.  A genetic link between co-suppression and RNA interference in C. elegans , 2000, Nature.

[8]  G. Macino,et al.  Homology-dependent gene silencing in plants and fungi: a number of variations on the same theme. , 1999, Current opinion in microbiology.

[9]  D. Anxolabéhère,et al.  Repression of hybrid dysgenesis in Drosophila melanogaster by combinations of telomeric P-element reporters and naturally occurring P elements. , 1998, Genetics.

[10]  R. Carthew,et al.  Use of dsRNA-Mediated Genetic Interference to Demonstrate that frizzled and frizzled 2 Act in the Wingless Pathway , 1998, Cell.

[11]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[12]  D. Petrov,et al.  Genomic regulation of transposable elements in Drosophila. , 1995, Current opinion in genetics & development.

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

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

[15]  Michel Labouesse,et al.  RNA interference: genetic wand and genetic watchdog , 2000, Nature Cell Biology.

[16]  E. Meyerowitz,et al.  Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[17]  A. Fire,et al.  Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference. , 2000, Molecular cell.

[18]  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.

[19]  R. Beeman,et al.  Analysis of maxillopedia expression pattern and larval cuticular phenotype in wild-type and mutant tribolium. , 2000, Genetics.

[20]  J. Nap,et al.  Detailed characterization of the posttranscriptional gene-silencing-related small RNA in a GUS gene-silenced tobacco. , 2000, RNA.

[21]  A. Mallory,et al.  A calmodulin-related protein that suppresses posttranscriptional gene silencing in plants. , 2000, Science.

[22]  A. Bucheton,et al.  New insights on homology-dependent silencing of I factor activity by transgenes containing ORF1 in Drosophila melanogaster. , 2000, Genetics.

[23]  K. Kemphues,et al.  par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed , 1995, Cell.

[24]  T. Pélissier,et al.  A DNA target of 30 bp is sufficient for RNA-directed DNA methylation. , 2000, RNA.

[25]  H. Vaucheret,et al.  AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[26]  R. Lehmann,et al.  Targeted mRNA degradation by double-stranded RNA in vitro. , 1999, Genes & development.

[27]  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.

[28]  J. Belote,et al.  Temperature‐dependent gene silencing by an expressed inverted repeat in Drosophila , 2000, Genesis.

[29]  A. Mccarthy.  Development , 1996, Current Opinion in Neurobiology.

[30]  C. Mello,et al.  RNAi in C. elegans: Soaking in the Genome Sequence , 1998, Science.

[31]  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.

[32]  J. Lohmann,et al.  Silencing of developmental genes in Hydra. , 1999, Developmental biology.

[33]  P. Waterhouse,et al.  Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[34]  K. Ui-Tei,et al.  Sensitive assay of RNA interference in Drosophila and Chinese hamster cultured cells using firefly luciferase gene as target , 2000, FEBS letters.

[35]  P. Sharp,et al.  RNAi and double-strand RNA. , 1999, Genes & development.

[36]  Juliette Gardner.  Genesis , 1985 .

[37]  Susan J. Brown,et al.  Using RNAi to investigate orthologous homeotic gene function during development of distantly related insects , 1999, Evolution & development.

[38]  Hugh D. Robertson,et al.  Escherichia coli ribonuclease III cleavage sites , 1982, Cell.

[39]  Olivier Voinnet,et al.  A Viral Movement Protein Prevents Spread of the Gene Silencing Signal in Nicotiana benthamiana , 2000, Cell.

[40]  M. Taira,et al.  RNA interference for the organizer-specific gene Xlim-1 in Xenopus embryos. , 2000, Biochemical and biophysical research communications.

[41]  A. Bateman,et al.  Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain. , 2000, Trends in biochemical sciences.

[42]  C. Mello,et al.  Genetic requirements for inheritance of RNAi in C. elegans. , 2000, Science.

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

[44]  C. Llave,et al.  Virus-encoded suppressor of posttranscriptional gene silencing targets a maintenance step in the silencing pathway. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[45]  J. Birchler,et al.  Making noise about silence: repression of repeated genes in animals. , 2000, Current opinion in genetics & development.

[46]  A. Fire,et al.  RNA-triggered gene silencing. , 1999, Trends in genetics : TIG.

[47]  A. Wargelius,et al.  Double-stranded RNA induces specific developmental defects in zebrafish embryos. , 1999, Biochemical and biophysical research communications.

[48]  G. Macino,et al.  Posttranscriptional gene silencing in Neurospora by a RecQ DNA helicase. , 1999, Science.

[49]  V. Georgiev.  Virology , 1955, Nature.

[50]  C. Gross,et al.  The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized. , 1999, Genes & development.

[51]  J. C. Clemens,et al.  Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[52]  H. L. Sänger,et al.  Isolation of an RNA-Directed RNA Polymerase–Specific cDNA Clone from Tomato , 1998, Plant Cell.

[53]  T. Kaufman,et al.  RNAi analysis of Deformed, proboscipedia and Sex combs reduced in the milkweed bug Oncopeltus fasciatus: novel roles for Hox genes in the hemipteran head. , 2000, Development.

[54]  B. Bainbridge,et al.  Genetics , 1981, Experientia.

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

[56]  A. Lucy,et al.  Suppression of post‐transcriptional gene silencing by a plant viral protein localized in the nucleus , 2000, The EMBO journal.

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

[58]  H. Vaucheret,et al.  Transgenes are dispensable for the RNA degradation step of cosuppression. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[59]  G. Macino,et al.  Transcription: Gene silencing in worms and fungi , 2000, Nature.

[60]  C. Hunter,et al.  Gene silencing: Shrinking the black box of RNAi , 2000, Current Biology.

[61]  Nektarios Tavernarakis,et al.  Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes , 2000, Nature Genetics.

[62]  R. Carthew,et al.  Heritable gene silencing in Drosophila using double-stranded RNA , 2000, Nature Biotechnology.

[63]  T. Blumenthal,et al.  U2AF35 is encoded by an essential gene clustered in an operon with RRM/cyclophilin in Caenorhabditis elegans. , 1999, RNA.

[64]  D. Baulcombe,et al.  Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[65]  T. Sijen,et al.  Post‐transcriptional gene‐silencing: RNAs on the attack or on the defense? , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[66]  R. Schultz,et al.  Selective reduction of dormant maternal mRNAs in mouse oocytes by RNA interference. , 2000, Development.

[67]  B. Williams,et al.  Interferon action in triply deficient mice reveals the existence of alternative antiviral pathways. , 1999, Virology.

[68]  R. Ho,et al.  Too much interference: injection of double-stranded RNA has nonspecific effects in the zebrafish embryo. , 2000, Developmental biology.

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

[70]  T. Heidmann,et al.  Cosuppression of I transposon activity in Drosophila by I-containing sense and antisense transgenes. , 1999, Genetics.

[71]  M. Ishizuka,et al.  A transgene with repeated DNA causes high frequency, post-transcriptional suppression of ACC-oxidase gene expression in tomato. , 1998, The Plant journal : for cell and molecular biology.

[72]  G. Stark,et al.  How cells respond to interferons. , 1998, Annual review of biochemistry.

[73]  P. Sharp,et al.  RNAi Double-Stranded RNA Directs the ATP-Dependent Cleavage of mRNA at 21 to 23 Nucleotide Intervals , 2000, Cell.

[74]  E. Robertis,et al.  The evolutionarily conserved BMP-binding protein Twisted gastrulation promotes BMP signalling , 2000, Nature.

[75]  G. Macino,et al.  Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase , 1999, Nature.

[76]  P. Mourrain,et al.  Arabidopsis Mutants Impaired in Cosuppression , 1998, Plant Cell.

[77]  P. Zipperlen,et al.  Functional genomic analysis of C. elegans chromosome I by systematic RNA interference , 2000, Nature.

[78]  A. Villeneuve,et al.  Transgene-mediated cosuppression in the C. elegans germ line. , 2000, Genes & development.

[79]  B. Bass.  Double-Stranded RNA as a Template for Gene Silencing , 2000, Cell.

[80]  A. Fire,et al.  RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[81]  A. Djikeng,et al.  Genetic interference in Trypanosoma brucei by heritable and inducible double-stranded RNA. , 2000, RNA.

[82]  M. Matzke,et al.  Listening to the silent genes: transgene silencing, gene regulation and pathogen control. , 1999, Trends in plant science.

[83]  S. Mango,et al.  A link between RNA interference and nonsense-mediated decay in Caenorhabditis elegans. , 2000, Science.

[84]  D. Baulcombe,et al.  Gene Silencing without DNA: RNA-Mediated Cross-Protection between Viruses , 1999, Plant Cell.

[85]  T. Heidmann,et al.  Taming of transposable elements by homology-dependent gene silencing , 1999, Nature Genetics.

[86]  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.

[87]  A. Fire,et al.  dsRNA-mediated gene silencing in cultured Drosophila cells: a tissue culture model for the analysis of RNA interference. , 2000, Gene.

[88]  Sebastian A. Leidel,et al.  Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III , 2000, Nature.

[89]  Jill M. Spoerke,et al.  EGO-1 is related to RNA-directed RNA polymerase and functions in germ-line development and RNA interference in C. elegans , 2000, Current Biology.

[90]  M. Kirby,et al.  Double-stranded RNA injection produces null phenotypes in zebrafish. , 2000, Developmental biology.

[91]  V. Solovyev,et al.  A novel type of RNase III family proteins in eukaryotes. , 2000, Gene.

[92]  J. Erickson,et al.  Evidence that processed small dsRNAs may mediate sequence-specific mRNA degradation during RNAi in Drosophila embryos , 2000, Current Biology.

[93]  S. Jacobsen,et al.  Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. , 1999, Development.