Book contents
- Frontmatter
- Contents
- Foreword by Andrew Fire
- Foreword by Marshall Nirenberg
- List of Contributors
- Introduction
- Section one Basic RNAi, siRNA, microRNAs and gene-silencing mechanisms
- 1 RNAi beginnings, Overview of the pathway in C. elegans
- 2 Dicer in RNAi: Its roles in vivo and utility in vitro
- 3 Genes required for RNA interference
- 4 MicroRNAs: A small contribution from worms
- 5 miRNAs in the brain and the application of RNAi to neurons
- Section two Design, synthesis of siRNAs
- Section three Vector development and in vivo, in vitro and in ovo delivery methods
- Section four Gene silencing in model organisms
- Section five Drug target validation
- Section six Therapeutic and drug development
- Section seven High-throughput genome-wide RNAi analysis
- Index
- Plate section
- References
1 - RNAi beginnings, Overview of the pathway in C. elegans
Published online by Cambridge University Press: 31 July 2009
Book contents
- Frontmatter
- Contents
- Foreword by Andrew Fire
- Foreword by Marshall Nirenberg
- List of Contributors
- Introduction
- Section one Basic RNAi, siRNA, microRNAs and gene-silencing mechanisms
- 1 RNAi beginnings, Overview of the pathway in C. elegans
- 2 Dicer in RNAi: Its roles in vivo and utility in vitro
- 3 Genes required for RNA interference
- 4 MicroRNAs: A small contribution from worms
- 5 miRNAs in the brain and the application of RNAi to neurons
- Section two Design, synthesis of siRNAs
- Section three Vector development and in vivo, in vitro and in ovo delivery methods
- Section four Gene silencing in model organisms
- Section five Drug target validation
- Section six Therapeutic and drug development
- Section seven High-throughput genome-wide RNAi analysis
- Index
- Plate section
- References
Summary
Introduction
The term “RNA interference” (RNAi) was coined by Andy Fire and Craig Mello to describe a sequence-specific gene silencing phenomenon of remarkable potency. They originally identified the main features of RNAi in C. elegans: initiation by double-stranded RNA (dsRNA) and ability to spread systemically (Fire et al., 1998). RNAi is recognized now as an ancient mechanism utilized by metazoans for silencing of foreign genetic elements and for the precise regulation of endogenous genes during development.
Initial studies of RNAi in C. elegans indicated that silencing was transient, did not affect the sequence of genomic DNA, and likely targeted mature mRNA (Fire et al., 1998; Montgomery et al., 1998). These observations identified RNAi as a sequence specific post-transcriptional gene silencing (PTGS) mechanism similar to those described in plants and fungi (Montgomery and Fire, 1998). The discovery of 21–25 nt long short interfering RNAs (siRNAs) as common intermediates in PTGS (Hamilton and Baulcombe, 1999) and RNAi (Zamore et al., 2000; Parrish et al., 2000; Tijsterman et al., 2002) further confirmed shared mechanistic features of sequence-specific silencing processes.
Steps of RNAi pathway in C. elegans
The remarkable response to introduction of just a few molecules of dsRNA per cell in C. elegans (Fire et al., 1998) suggested the existence of a pathway of genes responsible for the silencing process at the level of the whole organism. Screens for RNAi deficient (rde) mutants in the Mello lab (Tabara et al., 1999) identified two categories of mutants.
- Type
- Chapter
- Information
- RNA Interference TechnologyFrom Basic Science to Drug Development, pp. 17 - 28Publisher: Cambridge University PressPrint publication year: 2005
References
, , , and (2003). MicroRNAs and other tiny endogenous RNAs in C. elegans. Current Biology, 13, 807–818CrossRefGoogle ScholarPubMed
, , , , and (2001). Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Current Biology, 11, 1017–1027CrossRefGoogle ScholarPubMed
, , and (2001). Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363–366CrossRefGoogle ScholarPubMed
, , and (2002). Involvement of small RNAs and role of the genes in the gene silencing pathway in Neurospora. Genes & Development, 16, 790–795CrossRefGoogle ScholarPubMed
, , , , , , , , and (2003). A micrococcal nuclease homologue in RNAi effector complexes. Nature, 425, 411–414CrossRefGoogle ScholarPubMed
, , and (2002). Fragile X-related protein and VIG associate with the RNA interference machinery. Genes & Development, 16, 2491–2496CrossRefGoogle ScholarPubMed
and (2001). dpl-1 DP and efl-1 E2F act with lin-35 Rb to antagonize Ras signaling in C. elegans vulval development. Molecular Cell, 7, 461–473CrossRefGoogle ScholarPubMed
, and (1987). Activation of a transposable element in the germ line but not the soma of Caenorhabditis elegans. Nature, 328, 726–728CrossRefGoogle Scholar
, , and (2002). A heterochromatin protein 1 homologue in Caenorhabditis elegans acts in germline and vulval development. European Molecular Biology Organization Reports, 3, 235–241Google ScholarPubMed
, , , and (2000). An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell, 101, 543–553CrossRefGoogle Scholar
, , and (2000). Transgene-mediated cosuppression in the C. elegans germ line. Genes & Development, 14, 1578–1583Google ScholarPubMed
, , , and (2000). 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. Proceedings of the National Academy of Sciences USA, 97, 11650–11654CrossRefGoogle ScholarPubMed
, , , , and (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806–811CrossRefGoogle ScholarPubMed
, , , , , , , , , , , , , , , , , , , and (2000). Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature, 408, 331–336CrossRefGoogle Scholar
, and (2000). Genetic requirements for inheritance of RNAi in C. elegans. Science, 287, 2494–2497CrossRefGoogle ScholarPubMed
, , , , , , , , and (2001). Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell, 106, 23–34CrossRefGoogle ScholarPubMed
, , , , and (2002). Establishment and maintenance of a heterochromatin domain. Science, 297, 2232–2237CrossRefGoogle ScholarPubMed
and (1999). A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 286, 950–952CrossRefGoogle ScholarPubMed
, , and (2000). An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature, 404, 293–296CrossRefGoogle ScholarPubMed
, , , and (2001). Argonaute2, a link between genetic and biochemical analyses of RNAi. Science, 293, 1146–1150CrossRefGoogle ScholarPubMed
, and (1998). MES-2, a maternal protein essential for viability of the germline in Caenorhabditis elegans, is homologous to a Drosophila Polycomb group protein. Development, 125, 2457–2467Google ScholarPubMed
, , , , and (2001). A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science, 293, 834–838CrossRefGoogle ScholarPubMed
, , , , , , , , , , , and (2003). Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature, 421, 231–237CrossRefGoogle ScholarPubMed
and (1998). Chromatin silencing and the maintenance of a functional germline in Caenorhabditis elegans. Development, 125, 2451–2456Google ScholarPubMed
, , , , , and (2002). X-chromosome silencing in the germline of C. elegans. Development, 129, 479–492Google ScholarPubMed
, , and (1997). Distinct requirements for somatic and germline expression of a generally expressed Caernorhabditis elegans gene. Genetics, 146, 227–238Google ScholarPubMed
, , and (1999). Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNAseD. Cell, 99, 133–141CrossRefGoogle ScholarPubMed
and (2000). A genetic link between co-suppression and RNA interference in C. elegans. Nature, 404, 296–298CrossRefGoogle ScholarPubMed
, , , , and (2001). Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes & Development, 15, 2654–2659CrossRefGoogle ScholarPubMed
and (2001). A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science, 293, 2269–2271CrossRefGoogle ScholarPubMed
, and (1998). The Polycomb group in Caenorhabditis elegans and maternal control of germline development. Development, 125, 2469–2478Google ScholarPubMed
, , , , , and (2003). R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science, 301, 1921–1925CrossRefGoogle ScholarPubMed
, , and (2002). Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297, 2053–2056CrossRefGoogle ScholarPubMed
and (1998). lin-35 and lin-53, two genes that antagonize a C. elegans Ras pathway, encode proteins similar to Rb and its binding protein RbAp48. Cell, 95, 981–991CrossRefGoogle Scholar
, , , and (2002). Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell, 110, 563–574CrossRefGoogle ScholarPubMed
, , and (1991). Efficient gene transfer in C. elegans: Extra chromosomal maintenance and integration of transforming sequences. European Molecular Biology Organization Journal, 10, 3959–3970Google Scholar
and (1998). Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends in Genetics, 14, 255–258CrossRefGoogle ScholarPubMed
, and (1998). RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Proceedings of the National Academy of Sciences USA, 95, 15502–15507CrossRefGoogle ScholarPubMed
, , , , , , , , , , , , and (2000). Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell, 101, 533–542CrossRefGoogle ScholarPubMed
, and (1990). Introduction of a chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell, 2, 279–289CrossRefGoogle ScholarPubMed
, and (2001). ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell, 107, 309–321CrossRefGoogle ScholarPubMed
and (2001). Distinct roles for RDE-1 and RDE-4 during RNA interference in Caenorhabditis elegans. RNA, 7, 1397–13402Google ScholarPubMed
, , , and (2000). Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference. Molecular Cell, 6, 1077–1087CrossRefGoogle ScholarPubMed
, , and (2001). Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. Genetics, 157, 1217–1226Google ScholarPubMed
and (2002). Small RNAs correspond to centromere heterochromatic repeats. Science, 297, 1831CrossRefGoogle ScholarPubMed
, , , , and (2002). Prediction of plant microRNA targets. Cell, 110, 513–520CrossRefGoogle ScholarPubMed
and (2000). Molecular biology of RNA interference. Science, 287, 2431–2433CrossRefGoogle ScholarPubMed
, , , , , , and (2001). On the role of RNA amplification in dsRNA-triggered gene silencing. Cell, 107, 465–476CrossRefGoogle ScholarPubMed
, , , , , , and (2002). Loss of the putative RNA-directed RNA polymerase RRF-3 makes C. elegans hypersensitive to RNAi. Current Biology, 12, 1317–1319CrossRefGoogle ScholarPubMed
, , , , and (2000). EGO-1 is related to RNA-directed RNA polymerase and functions in germ-line development and RNA interference in C. elegans. Current Biology, 10, 169–178CrossRefGoogle ScholarPubMed
, , , , , , and (1999). The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell, 99, 123–132CrossRefGoogle ScholarPubMed
, , and (2002). The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans. Cell, 109, 861–871CrossRefGoogle Scholar
, , , and (2002). RNA helicase MUT-14-dependent gene silencing triggered in C. elegans by short antisense RNAs. Science, 295, 694–697CrossRefGoogle Scholar
, , , and (1990). Flavoid genes in Petunia: Addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell, 2, 291–299CrossRefGoogle Scholar
, , , , and (2002). Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science, 297, 1833–1837CrossRefGoogle ScholarPubMed
and (2002). ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos. Proceedings of the National Academy of Sciences USA, 99, 6889–6894CrossRefGoogle ScholarPubMed
, and (2002). Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science, 295, 2456–2459CrossRefGoogle Scholar
, , and (2000). RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101, 25–33CrossRefGoogle ScholarPubMed