RNA interference is an antiviral defence mechanism in Caenorhabditis elegans.

Department of Microbiology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA.
Nature (Impact Factor: 42.35). 09/2005; 436(7053):1044-7. DOI: 10.1038/nature03957
Source: PubMed

ABSTRACT RNA interference (RNAi) is an evolutionarily conserved sequence-specific post-transcriptional gene silencing mechanism that is well defined genetically in Caenorhabditis elegans. RNAi has been postulated to function as an adaptive antiviral immune mechanism in the worm, but there is no experimental evidence for this. Part of the limitation is that there are no known natural viral pathogens of C. elegans. Here we describe an infection model in C. elegans using the mammalian pathogen vesicular stomatitis virus (VSV) to study the role of RNAi in antiviral immunity. VSV infection is potentiated in cells derived from RNAi-defective worm mutants (rde-1; rde-4), leading to the production of infectious progeny virus, and is inhibited in mutants with an enhanced RNAi response (rrf-3; eri-1). Because the RNAi response occurs in the absence of exogenously added VSV small interfering RNAs, these results show that RNAi is activated during VSV infection and that RNAi is a genuine antiviral immune defence mechanism in the worm.

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    ABSTRACT: In various organisms, an efficient RNAi response can be triggered by feeding cells with bacteria producing double-stranded RNA (dsRNA) against an endogenous gene. However, the detailed mechanisms and natural functions of this pathway are not well understood in most cases. Here, we studied siRNA biogenesis from exogenous RNA and its genetic overlap with endogenous RNAi in the ciliate Paramecium tetraurelia by high-throughput sequencing. Using wild-type and mutant strains deficient for dsRNA feeding we found that high levels of primary siRNAs of both strands are processed from the ingested dsRNA trigger by the Dicer Dcr1, the RNA-dependent RNA polymerases Rdr1 and Rdr2 and other factors. We further show that this induces the synthesis of secondary siRNAs spreading along the entire endogenous mRNA, demonstrating the occurrence of both 3'-to-5' and 5'-to-3' transitivity for the first time in the SAR clade of eukaryotes (Stramenopiles, Alveolates, Rhizaria). Secondary siRNAs depend on Rdr2 and show a strong antisense bias; they are produced at much lower levels than primary siRNAs and hardly contribute to RNAi efficiency. We further provide evidence that the Paramecium RNAi machinery also processes single-stranded RNAs from its bacterial food, broadening the possible natural functions of exogenously induced RNAi in this organism. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
    Nucleic Acids Research 01/2015; 43(3). DOI:10.1093/nar/gku1331 · 8.81 Impact Factor
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    ABSTRACT: RNA interference (RNAi) has changed the traditional model of gene regulation by revealing the existence of small regulatory RNA fragments, known as small RNAs (sRNAs), which influence gene expression at the transcriptional and post transcriptional level. The study of sRNAs is currently carried out as a joint effort in molecular biology, high throughput sequencing, bioinformatics analysis and biochemical studies. The book covers these aspects in its three parts: Basics (chapters 1 - 8), Methods (chapters 9 - 15) and Applications (chapters 16 - 21) in an attempt to present a snapshot of a dynamic and prolific field. The first part commences with an overview of the known classes of sRNAs in “Renaissance of the regulatory RNAs”. The junk DNA is reconsidered and further classified into several types of non-coding regulatory RNAs. The brief description of microRNAs, siRNA, piRNA, snoRNA forming the first chapter is smoothly continued in the second chapter “Diversity, overlap and relationships in the small RNA landscape”. Here further details on the biogenesis and mode of actions of sRNAs are presented next to an analysis of the evolutionary relationship between transposable elements and sRNAs. The third chapter explores yet another class of sRNAs, the small nucleolar RNAs (snoRNAs) and highlights high throughput sequencing and RNA protection experiments as methods to facilitate the understanding of their mode of action. The forth chapter focuses on sRNAs in prokaryotes and systematically presents the few known sRNAs in bacteria. Their biogenesis, mode of actions and evolutionary analysis are extended with their integration in regulatory circuits. sRNAs regulating gene expressions through complementary base pairing and sRNAs that bind small proteins are described in detail. Chapters 5, 7, 8 return to eukaryotes and present particular types of sRNA in animals (chapter 5), in neural differentiation and plasticity (chapter 7) and in cancer (chapter 8). In chapter 6 an in-depth description of long non-coding RNAs is presented together with comments on their natural selection. The second part of the book, “Methods”, focusses on the computational methods developed for the analysis of high throughput data sets. The first two chapters introduce two widely used high throughput methods, microarrays and deep sequencing, the first being described in the context of LNA/DNA microarrays and ribonucleoprotein libraries (RNP) and the latter in the context of protocols and tools for improving the quality of second generation sequencing. The preparation of immunoprecipitation libraries and technical aspects including capturing sRNA populations with different 5’ and 3’ ends, reduction of adapter dimers and cross mapping of miRNA variants are discussed in detail. Chapters 11 and 12 describe the identification of targets in bacteria (chapter 11) and eukaryotes using overexpression and knock-down methods as well as target validation for 3’ UTR sites using luciferase reporters (chapter 12). Chapter 13 presents the identification of lncRNAs using computational (like de novo prediction from genomic sequences) and experimental approaches (such as lncRNA specific microarray and RNA immunoprecipitation). Chapter 14 focuses on RNA based regulation in bacteria describing the anti-sense transcription as a main mode of action and the resulting sRNAs are presented as components of regulatory circuits. The methods part concludes with the in depth description of microregulators from stem cells (chapter 15). This chapter focusses on the better understood class of microRNAs which are, in this context, linked to significant epigenetic regulation. The third part of the book, “Applications”, focusses on sRNAs in biological systems. Chapter 16 presents the unique opportunity to silence cancer causing stem cells at a post transcriptional level using sRNAs. The authors also explore RNAi therapy against multi drug resistance genes in a state of art description of the field. Chapter 17 focusses on another aspect of stem cells and the role of microRNAs, microRNA mimics, microRNA antagonists, antisense RNA and siRNA on cell differentiation and regenerative medicine. This direction is continued in chapter 18 where the authors present the role of microRNAs in neurodegenerative diseases focussing on genomic scale analysis of conditions such as Alzheimer’s disease and other dementias. Next, chapter 19 comes as a summary and state of art of siRNA therapeutic design aimed at improving intracellular interactions with RNAi proteins. The section is concluded with two chapters on microRNAs. Chapter 20 focusses on artificial microRNAs and chapter 21 presents an overview of microRNAs involved in cancer. The book represents a valuable collection of articles that reflect the current knowledge in the RNAi field. It is useful for both biologists and bioinformaticians, researchers and students alike, and strengthens the links between molecular biology and bioinformatics.

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