Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi

Transposable elements are stretches of DNA that can move and multiply within the genome of an organism. The Caenorhabditis elegans genome contains multiple Tc1 transposons that jump in somatic cells, but are silenced in the germ line. Many mutants that have lost this silencing have also lost the ability to execute RNA interference (RNAi), a process whereby genes are suppressed by exposure to homologous double-stranded RNA (dsRNA). Here we show how RNAi causes transposon silencing in the nematode germ line. We find evidence for transposon-derived dsRNAs, in particular to the terminal inverted repeats, and show that these RNAs may derive from read-through transcription of entire transposable elements. Small interfering RNAs of Tc1 were detected. When a germline-expressed reporter gene is fused to a stretch of Tc1 sequence, this transgene is silenced in a manner dependent on functional mutator genes (mut-7, mut-16 and pk732). These results indicate that RNAi surveillance is triggered by fortuitous read-through transcription of dispersed Tc1 copies, which can form dsRNA as a result of ‘snap-back’ of the terminal inverted repeats. RNAi mediated by this dsRNA silences transposase gene expression.

[1]  G. Walker,et al.  Biosynthetic control of molecular weight in the polymerization of the octasaccharide subunits of succinoglycan, a symbiotically important exopolysaccharide of Rhizobium meliloti. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[2]  R. E. Tully,et al.  Beta-glucan synthesis in Bradyrhizobium japonicum: characterization of a new locus (ndvC) influencing beta-(1-->6) linkages , 1996, Journal of bacteriology.

[3]  A. Caudy,et al.  A micrococcal nuclease homologue in RNAi effector complexes , 2003, Nature.

[4]  J. Kaper,et al.  Construction of an eae deletion mutant of enteropathogenic Escherichia coli by using a positive-selection suicide vector , 1991, Infection and immunity.

[5]  Julie Ahringer,et al.  A Genome-Wide Screen Identifies 27 Genes Involved in Transposon Silencing in C. elegans , 2003, Current Biology.

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

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

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

[9]  Philip S. Stewart,et al.  Contributions of Antibiotic Penetration, Oxygen Limitation, and Low Metabolic Activity to Tolerance of Pseudomonas aeruginosa Biofilms to Ciprofloxacin and Tobramycin , 2003, Antimicrobial Agents and Chemotherapy.

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

[11]  B. Ersbøll,et al.  Quantification of biofilm structures by the novel computer program COMSTAT. , 2000, Microbiology.

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

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

[14]  B. Ersbøll,et al.  Experimental reproducibility in flow-chamber biofilms. , 2000, Microbiology.

[15]  Elizabeth Casey,et al.  Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. , 2001, Genetics.

[16]  K. Miller,et al.  Cyclic beta-glucans of members of the family Rhizobiaceae , 1994, Microbiological reviews.

[17]  Roberto Kolter,et al.  Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis , 1998, Molecular microbiology.

[18]  Titia Sijen,et al.  On the Role of RNA Amplification in dsRNA-Triggered Gene Silencing , 2001, Cell.

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

[20]  B. Christensen,et al.  Molecular tools for study of biofilm physiology. , 1999, Methods in enzymology.

[21]  T. Sijen,et al.  RNA-Mediated Virus Resistance: Role of Repeated Transgenes and Delineation of Targeted Regions. , 1996, The Plant cell.

[22]  Roger E. Bumgarner,et al.  Gene expression in Pseudomonas aeruginosa biofilms , 2001, Nature.

[23]  J. Costerton,et al.  Bacterial biofilms: a common cause of persistent infections. , 1999, Science.

[24]  R. Plasterk,et al.  Transposase is the only nematode protein required for in vitro transposition of Tc1. , 1996, Genes & development.

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

[26]  S. W. Emmons,et al.  Evidence for a transposon in caenorhabditis elegans , 1983, Cell.

[27]  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.

[28]  J. Szejtli.  The cyclodextrins and their applications in biotechnology , 1990 .

[29]  B. Bass,et al.  The role of RNA editing by ADARs in RNAi. , 2002, Molecular cell.

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

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

[32]  R. Simon,et al.  New derivatives of transposon Tn5 suitable for mobilization of replicons, generation of operon fusions and induction of genes in gram-negative bacteria. , 1989, Gene.

[33]  G. O’Toole,et al.  Microbial Biofilms: from Ecology to Molecular Genetics , 2000, Microbiology and Molecular Biology Reviews.

[34]  S. Molin,et al.  Alginate Overproduction Affects Pseudomonas aeruginosa Biofilm Structure and Function , 2001, Journal of bacteriology.

[35]  D. Weisblat,et al.  Stochastic WNT signaling between nonequivalent cells regulates adhesion but not fate in the two-cell leech embryo , 2001, Current Biology.

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

[37]  B. Alberts,et al.  Isolation of actin‐associated proteins from Caenorhabditis elegans oocytes and their localization in the early embryo , 1997, The EMBO journal.

[38]  D. Baulcombe,et al.  Suppression of Virus Accumulation in Transgenic Plants Exhibiting Silencing of Nuclear Genes. , 1996, The Plant cell.

[39]  J. Costerton,et al.  Bacterial resistance to antibiotics: the role of biofilms. , 1991, Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques.

[40]  G. Caetano-Anollés,et al.  Amplifying DNA with arbitrary oligonucleotide primers. , 1993, PCR methods and applications.

[41]  Jacques Monod,et al.  The genetic control and cytoplasmic expression of “Inducibility” in the synthesis of β-galactosidase by E. coli , 1959 .

[42]  Titia Sijen,et al.  RNA Helicase MUT-14-Dependent Gene Silencing Triggered in C. elegans by Short Antisense RNAs , 2002, Science.

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

[44]  W. G. Kelly,et al.  Chromatin silencing and the maintenance of a functional germline in Caenorhabditis elegans. , 1998, Development.

[45]  H. Schnabel,et al.  Ballistic transformation of Caenorhabditis elegans. , 1999, Gene.

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

[47]  R. Yaklich,et al.  Characterization of ndvD, the third gene involved in the synthesis of cyclic beta-(1 --> 3),(1 --> 6)-D-glucans in Bradyrhizobium japonicum. , 2002, Canadian journal of microbiology.

[48]  P. Stewart,et al.  Role of Antibiotic Penetration Limitation in Klebsiella pneumoniae Biofilm Resistance to Ampicillin and Ciprofloxacin , 2000, Antimicrobial Agents and Chemotherapy.

[49]  G. O’Toole,et al.  Mechanisms of biofilm resistance to antimicrobial agents. , 2001, Trends in microbiology.

[50]  R. Plasterk,et al.  Continuous exchange of sequence information between dispersed Tc1 transposons in the Caenorhabditis elegans genome. , 2003, Genetics.

[51]  T. Sijen,et al.  Transcriptional and posttranscriptional gene silencing are mechanistically related , 2001, Current Biology.

[52]  C. Mello,et al.  The dsRNA Binding Protein RDE-4 Interacts with RDE-1, DCR-1, and a DExH-Box Helicase to Direct RNAi in C. elegans , 2002, Cell.