- 1 Механизм
- 2 Биологические функции
- 3 Эволюция
- 4 Приложения
- 5 История
- 6 Внешние ссылки
- 7 Примечания
Различия между организмами
[[Файл:Rnai diagram retrovirology.png|thumb|300px|right|Рисунок иллюстрирует различия между сайлесингом генов у растений и животных. МикроРНК, экспрессирующиеся в организме или введенные экзогенно малые интерферирующие РНК процессируются ферментом dicer и поступают в RISC, который осуществляет сайленсинг генов.]]
Организмы отличаются по способности воспринимать чужеродные двуцепочечные РНК и использовать их в процессе РНК-интерференции. Эффекты РНК-интерференции у растений и C. elegans (но не у дрозофилы и млекопитающих) могут наследоваться, а могут быть системными. У растений система РНК-интерференции может распространять малые интерферирующие РНК по плазмодесмам (каналам в клеточных стенках, осуществляющих коммуникацию и транспорт). Наследование обеспечивается метилированием промоторов, измененный паттерн метилирования передается в результате деления дочерним клеткам. A broad general distinction between plants and animals lies in the targeting of endogenously produced miRNAs; in plants, miRNAs are usually perfectly or nearly perfectly complementary to their target genes and induce direct mRNA cleavage by RISC, while animals' miRNAs tend to be more divergent in sequence and induce translational repression. This translational effect may be produced by inhibiting the interactions of translation initiation factors with the messenger RNA’s polyadenine tail.
Some eukaryotic protozoa such as Leishmania major and Trypanosoma cruzi lack the RNAi pathway entirely. Most or all of the components are also missing in some fungi, most notably the model organism Saccharomyces cerevisiae. A recent study however reveals the presence of RNAi in other budding yeast species such as Saccharomyces castellii and Candida albicans, further demonstrating that inducing two RNAi-related proteins from S. castellii facilitates RNAi in S. cerevisiae. That certain ascomycetes and basidiomycetes are missing RNA interference pathways indicates that proteins required for RNA silencing have been lost independently from many fungal lineages, possibly due to the evolution of a novel pathway with similar function, or to the lack of selective advantage in certain niches.
Related prokaryotic systems
Gene expression in prokaryotes is influenced by an RNA-based system similar in some respects to RNAi. Here, RNA-encoding genes control mRNA abundance or translation by producing a complementary RNA that binds to an mRNA by base pairing. However these regulatory RNAs are not generally considered to be analogous to miRNAs because the dicer enzyme is not involved. It has been suggested that CRISPR systems in prokaryotes are analogous to eukaryotic RNA interference systems, although none of the protein components are orthologous.
RNA interference is a vital part of the immune response to viruses and other foreign genetic material, especially in plants where it may also prevent self-propagation by transposons. Plants such as Arabidopsis thaliana express multiple dicer homologs that are specialized to react differently when the plant is exposed to different types of viruses. Even before the RNAi pathway was fully understood, it was known that induced gene silencing in plants could spread throughout the plant in a systemic effect, and could be transferred from stock to scion plants via grafting. This phenomenon has since been recognized as a feature of the plant adaptive immune system, and allows the entire plant to respond to a virus after an initial localized encounter. In response, many plant viruses have evolved elaborate mechanisms that suppress the RNAi response in plant cells. These include viral proteins that bind short double-stranded RNA fragments with single-stranded overhang ends, such as those produced by the action of dicer. Some plant genomes also express endogenous siRNAs in response to infection by specific types of bacteria. These effects may be part of a generalized response to pathogens that downregulates any metabolic processes in the host that aid the infection process.
Although animals generally express fewer variants of the dicer enzyme than plants, RNAi in some animals has also been shown to produce an antiviral response. In both juvenile and adult Drosophila, RNA interference is important in antiviral innate immunity and is active against pathogens such as Drosophila X virus. A similar role in immunity may operate in C. elegans, as argonaute proteins are upregulated in response to viruses and worms that overexpress components of the RNAi pathway are resistant to viral infection.
The role of RNA interference in mammalian innate immunity is poorly understood, and relatively little data is available. However, the existence of viruses that encode genes able to suppress the RNAi response in mammalian cells may be evidence in favour of an RNAi-dependent mammalian immune response. However, this hypothesis of RNAi-mediated immunity in mammals has been challenged as poorly substantiated. Alternative functions for RNAi in mammalian viruses also exist, such as miRNAs expressed by the herpes virus that may act as heterochromatin organization triggers to mediate viral latency.
Downregulation of genes
Endogenously expressed miRNAs, including both intronic and intergenic miRNAs, are most important in translational repression and in the regulation of development, especially on the timing of morphogenesis and the maintenance of undifferentiated or incompletely differentiated cell types such as stem cells. The role of endogenously expressed miRNA in downregulating gene expression was first described in C. elegans in 1993. In plants this function was discovered when the "JAW microRNA" of Arabidopsis was shown to be involved in the regulation of several genes that control plant shape. In plants, the majority of genes regulated by miRNAs are transcription factors; thus miRNA activity is particularly wide-ranging and regulates entire gene networks during development by modulating the expression of key regulatory genes, including transcription factors as well as F-box proteins. In many organisms, including humans, miRNAs have also been linked to the formation of tumors and dysregulation of the cell cycle. Here, miRNAs can function as both oncogenes and tumor suppressors.
Upregulation of genes
RNA sequences (siRNA and miRNA) that are complementary to parts of a promoter can increase gene transcription, a phenomenon dubbed RNA activation. Part of the mechanism for how these RNA upregulate genes is known: dicer and argonaute are involved, and there is histone demethylation.
Based on parsimony-based phylogenetic analysis, the most recent common ancestor of all eukaryotes most likely already possessed an early RNA interference pathway; the absence of the pathway in certain eukaryotes is thought to be a derived characteristic. This ancestral RNAi system probably contained at least one dicer-like protein, one argonaute, one PIWI protein, and an RNA-dependent RNA polymerase that may have also played other cellular roles. A large-scale comparative genomics study likewise indicates that the eukaryotic crown group already possessed these components, which may then have had closer functional associations with generalized RNA degradation systems such as the exosome. This study also suggests that the RNA-binding argonaute protein family, which is shared among eukaryotes, most archaea, and at least some bacteria (such as Aquifex aeolicus), is homologous to and originally evolved from components of the translation initiation system.
The ancestral function of the RNAi system is generally agreed to have been immune defense against exogenous genetic elements such as transposons and viral genomes. Related functions such as histone modification may have already been present in the ancestor of modern eukaryotes, although other functions such as regulation of development by miRNA are thought to have evolved later.
RNA interference genes, as components of the antiviral innate immune system in many eukaryotes, are involved in an evolutionary arms race with viral genes. Some viruses have evolved mechanisms for suppressing the RNAi response in their host cells, an effect that has been noted particularly for plant viruses. Studies of evolutionary rates in Drosophila have shown that genes in the RNAi pathway are subject to strong directional selection and are among the fastest-evolving genes in the Drosophila genome.
The RNA interference pathway is often exploited in experimental biology to study the function of genes in cell culture and in vivo in model organisms. Double-stranded RNA is synthesized with a sequence complementary to a gene of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway. Using this mechanism, researchers can cause a drastic decrease in the expression of a targeted gene. Studying the effects of this decrease can show the physiological role of the gene product. Since RNAi may not totally abolish expression of the gene, this technique is sometimes referred as a "knockdown", to distinguish it from "knockout" procedures in which expression of a gene is entirely eliminated.
Extensive efforts in computational biology have been directed toward the design of successful dsRNA reagents that maximize gene knockdown but minimize "off-target" effects. Off-target effects arise when an introduced RNA has a base sequence that can pair with and thus reduce the expression of multiple genes at a time. Such problems occur more frequently when the dsRNA contains repetitive sequences. It has been estimated from studying the genomes of H. sapiens, C. elegans, and S. pombe that about 10% of possible siRNAs will have substantial off-target effects. A multitude of software tools have been developed implementing algorithms for the design of general, mammal-specific, and virus-specific siRNAs that are automatically checked for possible cross-reactivity.
Depending on the organism and experimental system, the exogenous RNA may be a long strand designed to be cleaved by dicer, or short RNAs designed to serve as siRNA substrates. In most mammalian cells, shorter RNAs are used because long double-stranded RNA molecules induce the mammalian interferon response, a form of innate immunity that reacts nonspecifically to foreign genetic material. Mouse oocytes and cells from early mouse embryos lack this reaction to exogenous dsRNA and are therefore a common model system for studying gene-knockdown effects in mammals. Specialized laboratory techniques have also been developed to improve the utility of RNAi in mammalian systems by avoiding the direct introduction of siRNA, for example, by stable transfection with a plasmid encoding the appropriate sequence from which siRNAs can be transcribed, or by more elaborate lentiviral vector systems allowing the inducible activation or deactivation of transcription, known as conditional RNAi.
Most functional genomics applications of RNAi in animals have used C. elegans and Drosophila, as these are the common model organisms in which RNAi is most effective. C. elegans is particularly useful for RNAi research for two reasons: firstly, the effects of the gene silencing are generally heritable, and secondly because delivery of the dsRNA is extremely simple. Through a mechanism whose details are poorly understood, bacteria such as E. coli that carry the desired dsRNA can be fed to the worms and will transfer their RNA payload to the worm via the intestinal tract. This "delivery by feeding" is just as effective at inducing gene silencing as more costly and time-consuming delivery methods, such as soaking the worms in dsRNA solution and injecting dsRNA into the gonads. Although delivery is more difficult in most other organisms, efforts are also underway to undertake large-scale genomic screening applications in cell culture with mammalian cells.
Approaches to the design of genome-wide RNAi libraries can require more sophistication than the design of a single siRNA for a defined set of experimental conditions. Artificial neural networks are frequently used to design siRNA libraries and to predict their likely efficiency at gene knockdown. Mass genomic screening is widely seen as a promising method for genome annotation and has triggered the development of high-throughput screening methods based on microarrays. However, the utility of these screens and the ability of techniques developed on model organisms to generalize to even closely related species has been questioned, for example from C. elegans to related parasitic nematodes.
Functional genomics using RNAi is a particularly attractive technique for genomic mapping and annotation in plants because many plants are polyploid, which presents substantial challenges for more traditional genetic engineering methods. For example, RNAi has been successfully used for functional genomics studies in bread wheat (which is hexaploid) as well as more common plant model systems Arabidopsis and maize.
It may be possible to exploit RNA interference in therapy. Although it is difficult to introduce long dsRNA strands into mammalian cells due to the interferon response, the use of short interfering RNA mimics has been more successful. Among the first applications to reach clinical trials were in the treatment of macular degeneration and respiratory syncytial virus, RNAi has also been shown to be effective in the reversal of induced liver failure in mouse models.
Other proposed clinical uses center on antiviral therapies, including topical microbicide treatments that use RNAi to treat infection (at Harvard University Medical School; in mice, so far) by herpes simplex virus type 2 and the inhibition of viral gene expression in cancerous cells, knockdown of host receptors and coreceptors for HIV, the silencing of hepatitis A and hepatitis B genes, silencing of influenza gene expression, and inhibition of measles viral replication. Potential treatments for neurodegenerative diseases have also been proposed, with particular attention being paid to the polyglutamine diseases such as Huntington's disease. RNA interference is also often seen as a promising way to treat cancer by silencing genes differentially upregulated in tumor cells or genes involved in cell division. A key area of research in the use of RNAi for clinical applications is the development of a safe delivery method, which to date has involved mainly viral vector systems similar to those suggested for gene therapy.
Despite the proliferation of promising cell culture studies for RNAi-based drugs, some concern has been raised regarding the safety of RNA interference, especially the potential for "off-target" effects in which a gene with a coincidentally similar sequence to the targeted gene is also repressed. A computational genomics study estimated that the error rate of off-target interactions is about 10%. One major study of liver disease in mice led to high death rates in the experimental animals, suggested by researchers to be the result of "oversaturation" of the dsRNA pathway, due to the use of shRNAs that have to be processed in the nucleus and exported to the cytoplasm using an active mechanism. All these are considerations that are under active investigation, to reduce their impact in the potential therapeutic applications for RNAi.
RNA interference has been used for applications in biotechnology, particularly in the engineering of food plants that produce lower levels of natural plant toxins. Such techniques take advantage of the stable and heritable RNAi phenotype in plant stocks. For example, cotton seeds are rich in dietary protein but naturally contain the toxic terpenoid product gossypol, making them unsuitable for human consumption. RNAi has been used to produce cotton stocks whose seeds contain reduced levels of delta-cadinene synthase, a key enzyme in gossypol production, without affecting the enzyme's production in other parts of the plant, where gossypol is important in preventing damage from plant pests. Similar efforts have been directed toward the reduction of the cyanogenic natural product linamarin in cassava plants.
Although no plant products that use RNAi-based genetic engineering have yet passed the experimental stage, development efforts have successfully reduced the levels of allergens in tomato plants and decreased the precursors of likely carcinogens in tobacco plants. Other plant traits that have been engineered in the laboratory include the production of non-narcotic natural products by the opium poppy, resistance to common plant viruses, and fortification of plants such as tomatoes with dietary antioxidants. Previous commercial products, including the Flavr Savr tomato and two cultivars of ringspot-resistant papaya, were originally developed using antisense technology but likely exploited the RNAi pathway.
The discovery of RNAi was preceded first by observations of transcriptional inhibition by antisense RNA expressed in transgenic plants, and more directly by reports of unexpected outcomes in experiments performed by plant scientists in the U.S. and The Netherlands in the early 1990s. In an attempt to alter flower colors in petunias, researchers introduced additional copies of a gene encoding chalcone synthase, a key enzyme for flower pigmentation into petunia plants of normally pink or violet flower color. The overexpressed gene was expected to result in darker flowers, but instead produced less pigmented, fully or partially white flowers, indicating that the activity of chalcone synthase had been substantially decreased; in fact, both the endogenous genes and the transgenes were downregulated in the white flowers. Soon after, a related event termed quelling was noted in the fungus Neurospora crassa, although it was not immediately recognized as related. Further investigation of the phenomenon in plants indicated that the downregulation was due to post-transcriptional inhibition of gene expression via an increased rate of mRNA degradation. This phenomenon was called co-suppression of gene expression, but the molecular mechanism remained unknown.
Not long after, plant virologists working on improving plant resistance to viral diseases observed a similar unexpected phenomenon. While it was known that plants expressing virus-specific proteins showed enhanced tolerance or resistance to viral infection, it was not expected that plants carrying only short, non-coding regions of viral RNA sequences would show similar levels of protection. Researchers believed that viral RNA produced by transgenes could also inhibit viral replication. The reverse experiment, in which short sequences of plant genes were introduced into viruses, showed that the targeted gene was suppressed in an infected plant. This phenomenon was labeled "virus-induced gene silencing" (VIGS), and the set of such phenomena were collectively called post transcriptional gene silencing.
After these initial observations in plants, many laboratories around the world searched for the occurrence of this phenomenon in other organisms. Craig C. Mello and Andrew Fire's 1998 Nature paper reported a potent gene silencing effect after injecting double stranded RNA into C. elegans. In investigating the regulation of muscle protein production, they observed that neither mRNA nor antisense RNA injections had an effect on protein production, but double-stranded RNA successfully silenced the targeted gene. As a result of this work, they coined the term RNAi. Fire and Mello's discovery was particularly notable because it represented the first identification of the causative agent for the phenomenon. Fire and Mello were awarded the Nobel Prize in Physiology or Medicine in 2006 for their work.
- Overview of the RNAi process, from Cambridge University's The Naked Scientists
- Animation of the RNAi process, from Nature
- NOVA scienceNOW explains RNAi – A 15 minute video of the Nova broadcast that aired on PBS, July 26, 2005
- Silencing Genomes RNA interference (RNAi) experiments and bioinformatics in C. elegans for education. From the Dolan DNA Learning Center of Cold Spring Harbor Laboratory.
- RNAi screens in C. elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions (a protocol)
- 2 American ‘Worm People’ Win Nobel for RNA Work, from NY Times
- Molecular Therapy web focus: "The development of RNAi as a therapeutic strategy" , a collection of free articles about RNAi as a therapeutic strategy.
- Saumet A, Lecellier CH (2006). "Anti-viral RNA silencing: do we look like plants?". Retrovirology. 3 (3): 3. doi:10.1186/1742-4690-3-3. PMID 16409629.
- Cite error: The named reference
Lodishwas invoked but never defined (see the help page).
- Jones L, Ratcliff F, Baulcombe DC (2001). "RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance". Current Biology. 11 (10): 747–757. doi:10.1016/S0960-9822(01)00226-3.
- Humphreys DT, Westman BJ, Martin DI, Preiss T (2005). "MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function". Proc Natl Acad Sci USA. 102: 16961–16966. doi:10.1073/pnas.0506482102. PMID 16287976.
- DaRocha W, Otsu K, Teixeira S, Donelson J (2004). "Tests of cytoplasmic RNA interference (RNAi) and construction of a tetracycline-inducible T7 promoter system in Trypanosoma cruzi". Mol Biochem Parasitol. 133 (2): 175–86. doi:10.1016/j.molbiopara.2003.10.005. PMID 14698430.
- Robinson K, Beverley S (2003). "Improvements in transfection efficiency and tests of RNA interference (RNAi) approaches in the protozoan parasite Leishmania". Mol Biochem Parasitol. 128 (2): 217–28. doi:10.1016/S0166-6851(03)00079-3. PMID 12742588.
- L. Aravind, Hidemi Watanabe, David J. Lipman, and Eugene V. Koonin (2000). "Lineage-specific loss and divergence of functionally linked genes in eukaryotes". Proceedings of the National Academy of Sciences. 97 (21): 11319–11324. doi:10.1073/pnas.200346997. PMID 11016957.
- Drinnenberg IA, Weinberg DE, Xie KT, Nower JP, Wolfe KH, Fink GR, Bartel DP (2009). "RNAi in Budding Yeast". Science. doi:10.1126/science.1176945. PMID 19745116.
- Nakayashiki H, Kadotani N, Mayama S (2006). "Evolution and diversification of RNA silencing proteins in fungi". J Mol Evol. 63 (1): 127–35. doi:10.1007/s00239-005-0257-2. PMID 16786437.
- Morita T, Mochizuki Y, Aiba H (2006). "Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction". Proc Natl Acad Sci USA. 103 (13): 4858–63. doi:10.1073/pnas.0509638103. PMID 16549791.
- Makarova K, Grishin N, Shabalina S, Wolf Y, Koonin E (2006). "A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action". Biol Direct. 1: 7. doi:10.1186/1745-6150-1-7. PMID 16545108.
- Stram Y, Kuzntzova L (2006). "Inhibition of viruses by RNA interference". Virus Genes. 32 (3): 299–306. doi:10.1007/s11262-005-6914-0. PMID 16732482.
- Blevins T, Rajeswaran R, Shivaprasad P, Beknazariants D, Si-Ammour A, Park H, Vazquez F, Robertson D, Meins F, Hohn T, Pooggin M (2006). "Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing". Nucleic Acids Res. 34 (21): 6233–46. doi:10.1093/nar/gkl886. PMID 17090584.
- Palauqui J, Elmayan T, Pollien J, Vaucheret H (1997). "Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions". EMBO J. 16 (15): 4738–45. doi:10.1093/emboj/16.15.4738. PMID 9303318.
- Voinnet O (2001). "RNA silencing as a plant immune system against viruses". Trends Genet. 17 (8): 449–59. doi:10.1016/S0168-9525(01)02367-8. PMID 11485817.
- Lucy A, Guo H, Li W, Ding S (2000). "Suppression of post-transcriptional gene silencing by a plant viral protein localized in the nucleus". EMBO J. 19 (7): 1672–80. doi:10.1093/emboj/19.7.1672. PMID 10747034.
- Mérai Z, Kerényi Z, Kertész S, Magna M, Lakatos L, Silhavy D (2006). "Double-stranded RNA binding may be a general plant RNA viral strategy to suppress RNA silencing". J Virol. 80 (12): 5747–56. doi:10.1128/JVI.01963-05. PMID 16731914.
- Katiyar-Agarwal S, Morgan R, Dahlbeck D, Borsani O, Villegas A, Zhu J, Staskawicz B, Jin H (2006). "A pathogen-inducible endogenous siRNA in plant immunity". Proc Natl Acad Sci USA. 103 (47): 18002–7. doi:10.1073/pnas.0608258103. PMID 17071740.
- Fritz J, Girardin S, Philpott D (2006). "Innate immune defense through RNA interference". Sci STKE. 2006 (339): pe27. doi:10.1126/stke.3392006pe27. PMID 16772641.
- Zambon R, Vakharia V, Wu L (2006). "RNAi is an antiviral immune response against a dsRNA virus in Drosophila melanogaster". Cell Microbiol. 8 (5): 880–9. doi:10.1111/j.1462-5822.2006.00688.x. PMID 16611236.
- Wang X, Aliyari R, Li W, Li H, Kim K, Carthew R, Atkinson P, Ding S (2006). "RNA interference directs innate immunity against viruses in adult Drosophila". Science. 312 (5772): 452–4. doi:10.1126/science.1125694. PMID 16556799.
- Lu R, Maduro M, Li F, Li H, Broitman-Maduro G, Li W, Ding S (2005). "Animal virus replication and RNAi-mediated antiviral silencing in Caenorhabditis elegans". Nature. 436 (7053): 1040–3. doi:10.1038/nature03870. PMID 16107851.
- Wilkins C, Dishongh R, Moore S, Whitt M, Chow M, Machaca K (2005). "RNA interference is an antiviral defence mechanism in Caenorhabditis elegans". Nature. 436 (7053): 1044–7. doi:10.1038/nature03957. PMID 16107852.
- Berkhout B, Haasnoot J (2006). "The interplay between virus infection and the cellular RNA interference machinery". FEBS Lett. 580 (12): 2896–902. doi:10.1016/j.febslet.2006.02.070. PMID 16563388.
- Schütz S, Sarnow P (2006). "Interaction of viruses with the mammalian RNA interference pathway". Virology. 344 (1): 151–7. doi:10.1016/j.virol.2005.09.034. PMID 16364746.
- Cullen B (2006). "Is RNA interference involved in intrinsic antiviral immunity in mammals?". Nat Immunol. 7 (6): 563–7. doi:10.1038/ni1352. PMID 16715068.
- Li H, Ding S (2005). "Antiviral silencing in animals". FEBS Lett. 579 (26): 5965–73. doi:10.1016/j.febslet.2005.08.034. PMID 16154568. Cite error: Invalid
<ref>tag; name "Li" defined multiple times with different content (see the help page).
- Carrington J, Ambros V (2003). "Role of microRNAs in plant and animal development". Science. 301 (5631): 336–8. doi:10.1126/science.1085242. PMID 12869753.
- Lee R, Feinbaum R, Ambros V (1993). "The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14". Cell. 75 (5): 843–54. doi:10.1016/0092-8674(93)90529-Y. PMID 8252621.
- Palatnik J, Allen E, Wu X, Schommer C, Schwab R, Carrington J, Weigel D (2003). "Control of leaf morphogenesis by microRNAs". Nature. 425 (6955): 257–63. doi:10.1038/nature01958. PMID 12931144.
- Zhang B, Pan X, Cobb G, Anderson T (2006). "Plant microRNA: a small regulatory molecule with big impact". Dev Biol. 289 (1): 3–16. doi:10.1016/j.ydbio.2005.10.036. PMID 16325172.
- Jones-Rhoades M, Bartel D, Bartel B (2006). "MicroRNAS and their regulatory roles in plants". Annu Rev Plant Biol. 57: 19–53. doi:10.1146/annurev.arplant.57.032905.105218. PMID 16669754.
- Zhang B, Pan X, Cobb G, Anderson T (2007). "microRNAs as oncogenes and tumor suppressors". Dev Biol. 302 (1): 1–12. doi:10.1016/j.ydbio.2006.08.028. PMID 16989803.
- Check E (2007). "RNA interference: hitting the on switch". Nature. 448 (7156): 855–858. doi:10.1038/448855a. PMID 17713502.
- Li LC, Okino ST, Zhao H; et al. (2006). "Small dsRNAs induce transcriptional activation in human cells". Proc. Natl. Acad. Sci. U.S.A. 103 (46): 17337–42. doi:10.1073/pnas.0607015103. PMID 17085592.
- Cerutti H, Casas-Mollano J (2006). "On the origin and functions of RNA-mediated silencing: from protists to man". Curr Genet. 50 (2): 81–99. doi:10.1007/s00294-006-0078-x. PMID 16691418.
- Anantharaman V, Koonin E, Aravind L (2002). "Comparative genomics and evolution of proteins involved in RNA metabolism". Nucleic Acids Res. 30 (7): 1427–64. doi:10.1093/nar/30.7.1427. PMID 11917006.
- Buchon N, Vaury C (2006). "RNAi: a defensive RNA-silencing against viruses and transposable elements". Heredity. 96 (2): 195–202. doi:10.1038/sj.hdy.6800789. PMID 16369574.
- Obbard D, Jiggins F, Halligan D, Little T (2006). "Natural selection drives extremely rapid evolution in antiviral RNAi genes". Curr Biol. 16 (6): 580–5. doi:10.1016/j.cub.2006.01.065. PMID 16546082.
- Brock T, Browse J, Watts J (2006). "Genetic regulation of unsaturated fatty acid composition in C. elegans". PLoS Genet. 2 (7): e108. doi:10.1371/journal.pgen.0020108. PMID 16839188.
- Cite error: The named reference
Daneholt2006was invoked but never defined (see the help page).
- Voorhoeve PM, Agami R (2003). "Knockdown stands up". Trends Biotechnol. 21 (1): 2–4. doi:10.1016/S0167-7799(02)00002-1. PMID 12480342.
- Cite error: The named reference
Qiuwas invoked but never defined (see the help page).
- Naito Y, Yamada T, Matsumiya T, Ui-Tei K, Saigo K, Morishita S (2005). "dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference". Nucleic Acids Res. 33 (Web Server issue): W589–91. doi:10.1093/nar/gki419. PMID 15980542.
- Henschel A, Buchholz F, Habermann B (2004). "DEQOR: a web-based tool for the design and quality control of siRNAs". Nucleic Acids Res. 32 (Web Server issue): W113–20. doi:10.1093/nar/gkh408. PMID 15215362.
- Naito Y, Yamada T, Ui-Tei K, Morishita S, Saigo K (2004). "siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference". Nucleic Acids Res. 32 (Web Server issue): W124–9. doi:10.1093/nar/gkh442. PMID 15215364.
- Naito Y, Ui-Tei K, Nishikawa T, Takebe Y, Saigo K (2006). "siVirus: web-based antiviral siRNA design software for highly divergent viral sequences". Nucleic Acids Res. 34 (Web Server issue): W448–50. doi:10.1093/nar/gkl214. PMID 16845046.
- Reynolds A, Anderson E, Vermeulen A, Fedorov Y, Robinson K, Leake D, Karpilow J, Marshall W, Khvorova A (2006). "Induction of the interferon response by siRNA is cell type- and duplex length-dependent". RNA. 12 (6): 988–93. doi:10.1261/rna.2340906. PMID 16611941.
- Stein P, Zeng F, Pan H, Schultz R (2005). "Absence of non-specific effects of RNA interference triggered by long double-stranded RNA in mouse oocytes". Dev Biol. 286 (2): 464–71. doi:10.1016/j.ydbio.2005.08.015. PMID 16154556.
- Brummelkamp T, Bernards R, Agami R (2002). "A system for stable expression of short interfering RNAs in mammalian cells". Science. 296 (5567): 550–3. doi:10.1126/science.1068999. PMID 11910072.
- Tiscornia G, Tergaonkar V, Galimi F, Verma I (2004). "CRE recombinase-inducible RNA interference mediated by lentiviral vectors". Proc Natl Acad Sci USA. 101 (19): 7347–51. doi:10.1073/pnas.0402107101. PMID 15123829.
- Ventura A, Meissner A, Dillon C, McManus M, Sharp P, Van Parijs L, Jaenisch R, Jacks T (2004). "Cre-lox-regulated conditional RNA interference from transgenes". Proc Natl Acad Sci USA. 101 (28): 10380–5. doi:10.1073/pnas.0403954101. PMID 15240889.
- Kamath R, Ahringer J (2003). "Genome-wide RNAi screening in Caenorhabditis elegans". Methods. 30 (4): 313–21. doi:10.1016/S1046-2023(03)00050-1. PMID 12828945.
- Boutros M, Kiger A, Armknecht S, Kerr K, Hild M, Koch B, Haas S, Paro R, Perrimon N (2004). "Genome-wide RNAi analysis of growth and viability in Drosophila cells". Science. 303 (5659): 832–5. doi:10.1126/science.1091266. PMID 14764878.
- Fortunato A, Fraser A (2005). "Uncover genetic interactions in Caenorhabditis elegans by RNA interference". Biosci Rep. 25 (5–6): 299–307. doi:10.1007/s10540-005-2892-7. PMID 16307378.
- Cullen L, Arndt G (2005). "Genome-wide screening for gene function using RNAi in mammalian cells". Immunol Cell Biol. 83 (3): 217–23. doi:10.1111/j.1440-1711.2005.01332.x. PMID 15877598.
- Huesken D, Lange J, Mickanin C, Weiler J, Asselbergs F, Warner J, Meloon B, Engel S, Rosenberg A, Cohen D, Labow M, Reinhardt M, Natt F, Hall J (2005). "Design of a genome-wide siRNA library using an artificial neural network". Nat Biotechnol. 23 (8): 995–1001. doi:10.1038/nbt1118. PMID 16025102.
- Ge G, Wong G, Luo B (2005). "Prediction of siRNA knockdown efficiency using artificial neural network models". Biochem Biophys Res Commun. 336 (2): 723–8. doi:10.1016/j.bbrc.2005.08.147. PMID 16153609.
- Janitz M, Vanhecke D, Lehrach H (2006). "High-throughput RNA interference in functional genomics". Handb Exp Pharmacol. 173: 97–104. doi:10.1007/3-540-27262-3_5. PMID 16594612.
- Vanhecke D, Janitz M (2005). "Functional genomics using high-throughput RNA interference". Drug Discov Today. 10 (3): 205–12. doi:10.1016/S1359-6446(04)03352-5. PMID 15708535.
- Geldhof P, Murray L, Couthier A, Gilleard J, McLauchlan G, Knox D, Britton C (2006). "Testing the efficacy of RNA interference in Haemonchus contortus". Int J Parasitol. 36 (7): 801–10. doi:10.1016/j.ijpara.2005.12.004. PMID 16469321.
- Geldhof P, Visser A, Clark D, Saunders G, Britton C, Gilleard J, Berriman M, Knox D. (2007). "RNA interference in parasitic helminths: current situation, potential pitfalls and future prospects". Parasitology. 134: 1–11. doi:10.1017/S0031182006002071. PMID 17201997.
- Travella S, Klimm T, Keller B (2006). "RNA interference-based gene silencing as an efficient tool for functional genomics in hexaploid bread wheat". Plant Physiol. 142 (1): 6–20. doi:10.1104/pp.106.084517. PMID 16861570.
- McGinnis K, Chandler V, Cone K, Kaeppler H, Kaeppler S, Kerschen A, Pikaard C, Richards E, Sidorenko L, Smith T, Springer N, Wulan T (2005). "Transgene-induced RNA interference as a tool for plant functional genomics". Methods Enzymol. 392: 1–24. doi:10.1016/S0076-6879(04)92001-0. PMID 15644172.
- Paddison P, Caudy A, Hannon G (2002). "Stable suppression of gene expression by RNAi in mammalian cells". Proc Natl Acad Sci USA. 99 (3): 1443–8. doi:10.1073/pnas.032652399. PMID 11818553.
- Sah D (2006). "Therapeutic potential of RNA interference for neurological disorders". Life Sci. 79 (19): 1773–80. doi:10.1016/j.lfs.2006.06.011. PMID 16815477.
- Zender L, Hutker S, Liedtke C, Tillmann H, Zender S, Mundt B, Waltemathe M, Gosling T, Flemming P, Malek N, Trautwein C, Manns M, Kuhnel F, Kubicka S (2003). "Caspase 8 small interfering RNA prevents acute liver failure in mice". Proc Natl Acad Sci USA. 100 (13): 7797–802. doi:10.1073/pnas.1330920100. PMID 12810955.
- Jiang M, Milner J (2002). "Selective silencing of viral gene expression in HPV-positive human cervical carcinoma cells treated with siRNA, a primer of RNA interference". Oncogene. 21 (39): 6041–8. doi:10.1038/sj.onc.1205878. PMID 12203116.
- Crowe S (2003). "Suppression of chemokine receptor expression by RNA interference allows for inhibition of HIV-1 replication, by Martínez et al". AIDS. 17 Suppl 4: S103–5. PMID 15080188.
- Kusov Y, Kanda T, Palmenberg A, Sgro J, Gauss-Müller V (2006). "Silencing of hepatitis A virus infection by small interfering RNAs". J Virol. 80 (11): 5599–610. doi:10.1128/JVI.01773-05. PMID 16699041.
- Jia F, Zhang Y, Liu C (2006). "A retrovirus-based system to stably silence hepatitis B virus genes by RNA interference". Biotechnol Lett. 28 (20): 1679–85. doi:10.1007/s10529-006-9138-z. PMID 16900331.
- Hu L, Wang Z, Hu C, Liu X, Yao L, Li W, Qi Y (2005). "Inhibition of Measles virus multiplication in cell culture by RNA interference". Acta Virol. 49 (4): 227–34. PMID 16402679.
- Raoul C, Barker S, Aebischer P (2006). "Viral-based modelling and correction of neurodegenerative diseases by RNA interference". Gene Ther. 13 (6): 487–95. doi:10.1038/sj.gt.3302690. PMID 16319945.
- Putral L, Gu W, McMillan N (2006). "RNA interference for the treatment of cancer". Drug News Perspect. 19 (6): 317–24. doi:10.1358/dnp.2006.19.6.985937. PMID 16971967.
- Izquierdo M (2005). "Short interfering RNAs as a tool for cancer gene therapy". Cancer Gene Ther. 12 (3): 217–27. doi:10.1038/sj.cgt.7700791. PMID 15550938.
- Li C, Parker A, Menocal E, Xiang S, Borodyansky L, Fruehauf J (2006). "Delivery of RNA interference". Cell Cycle. 5 (18): 2103–9. PMID 16940756.
- Takeshita F, Ochiya T (2006). "Therapeutic potential of RNA interference against cancer". Cancer Sci. 97 (8): 689–96. doi:10.1111/j.1349-7006.2006.00234.x. PMID 16863503.
- Tong A, Zhang Y, Nemunaitis J (2005). "Small interfering RNA for experimental cancer therapy". Curr Opin Mol Ther. 7 (2): 114–24. PMID 15844618.
- Grimm D, Streetz K, Jopling C, Storm T, Pandey K, Davis C, Marion P, Salazar F, Kay M (2006). "Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways". Nature. 441 (7092): 537–41. doi:10.1038/nature04791. PMID 16724069.
- Sunilkumar G, Campbell L, Puckhaber L, Stipanovic R, Rathore K (2006). "Engineering cottonseed for use in human nutrition by tissue-specific reduction of toxic gossypol". Proc Natl Acad Sci USA. 103 (48): 18054–9. doi:10.1073/pnas.0605389103. PMID 17110445.
- Siritunga D, Sayre R (2003). "Generation of cyanogen-free transgenic cassava". Planta. 217 (3): 367–73. doi:10.1007/s00425-003-1005-8. PMID 14520563.
- Le L, Lorenz Y, Scheurer S, Fötisch K, Enrique E, Bartra J, Biemelt S, Vieths S, Sonnewald U (2006). "Design of tomato fruits with reduced allergenicity by dsRNAi-mediated inhibition of ns-LTP (Lyc e 3) expression". Plant Biotechnol J. 4 (2): 231–42. doi:10.1111/j.1467-7652.2005.00175.x. PMID 17177799.
- Gavilano L, Coleman N, Burnley L, Bowman M, Kalengamaliro N, Hayes A, Bush L, Siminszky B (2006). "Genetic engineering of Nicotiana tabacum for reduced nornicotine content". J Agric Food Chem. 54 (24): 9071–8. doi:10.1021/jf0610458. PMID 17117792.
- Allen R, Millgate A, Chitty J, Thisleton J, Miller J, Fist A, Gerlach W, Larkin P (2004). "RNAi-mediated replacement of morphine with the nonnarcotic alkaloid reticuline in opium poppy". Nat Biotechnol. 22 (12): 1559–66. doi:10.1038/nbt1033. PMID 15543134.
- Zadeh A, Foster G (2004). "Transgenic resistance to tobacco ringspot virus". Acta Virol. 48 (3): 145–52. PMID 15595207.
- Niggeweg R, Michael A, Martin C (2004). "Engineering plants with increased levels of the antioxidant chlorogenic acid". Nat Biotechnol. 22 (6): 746–54. doi:10.1038/nbt966. PMID 15107863.
- Sanders R, Hiatt W (2005). "Tomato transgene structure and silencing". Nat Biotechnol. 23 (3): 287–9. doi:10.1038/nbt0305-287b. PMID 15765076.
- Chiang C, Wang J, Jan F, Yeh S, Gonsalves D (2001). "Comparative reactions of recombinant papaya ringspot viruses with chimeric coat protein (CP) genes and wild-type viruses on CP-transgenic papaya". J Gen Virol. 82 (Pt 11): 2827–36. PMID 11602796.
- Matzke MA, Matzke AJM. (2004). "Planting the Seeds of a New Paradigm". PLoS Biol. 2 (5): e133. doi:10.1371/journal.pbio.0020133. PMID 15138502.
- Ecker JR, Davis RW (1986). "Inhibition of gene expression in plant cells by expression of antisense RNA". Proc Natl Acad Sci USA. 83 (15): 5372–5376. doi:10.1073/pnas.83.15.5372. PMID 16593734.
- Napoli C, Lemieux C, Jorgensen R (1990). "Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans". Plant Cell. 2 (4): 279–289. doi:10.1105/tpc.2.4.279. PMID 12354959.
- Romano N, Macino G (1992). "Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences". Mol Microbiol. 6 (22): 3343–53. doi:10.1111/j.1365-2958.1992.tb02202.x. PMID 1484489.
- Van Blokland R, Van der Geest N, Mol JNM, Kooter JM (1994). "Transgene-mediated suppression of chalcone synthase expression in Petunia hybrida results from an increase in RNA turnover". Plant J. 6: 861–77. doi:10.1046/j.1365-313X.1994.6060861.x/abs/.
- Mol JNM, van der Krol AR (1991). Antisense nucleic acids and proteins: fundamentals and applications. M. Dekker. pp. 4, 136. ISBN 0824785169.
- Covey S, Al-Kaff N, Lángara A, Turner D (1997). "Plants combat infection by gene silencing". Nature. 385: 781–2. doi:10.1038/385781a0.
- Ratcliff F, Harrison B, Baulcombe D (1997). "A Similarity Between Viral Defense and Gene Silencing in Plants". Science. 276: 1558–60. doi:10.1126/science.276.5318.1558.
- Guo S, Kemphues K (1995). "par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed". Cell. 81 (4): 611–20. doi:10.1016/0092-8674(95)90082-9. PMID 7758115.
- Pal-Bhadra M, Bhadra U, Birchler J (1997). "Cosuppression in Drosophila: gene silencing of Alcohol dehydrogenase by white-Adh transgenes is Polycomb dependent". Cell. 90 (3): 479–90. doi:10.1016/S0092-8674(00)80508-5. PMID 9267028.
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