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SLAS Discovery : Advancing Life... Jul 2020
Topics: CRISPR-Cas Systems; Genomics; Humans; RNA Interference; RNA, Small Interfering
PubMed: 32567999
DOI: 10.1177/2472555220927692 -
Biotechnology Advances 2020RNA interference (RNAi) is a biological process in which small RNA (sRNA) molecules sequence-specifically silence gene expression at the transcriptional or... (Review)
Review
RNA interference (RNAi) is a biological process in which small RNA (sRNA) molecules sequence-specifically silence gene expression at the transcriptional or post-transcriptional level, either by directing inhibitory chromatin modifications or by decreasing the stability or translation potential of the targeted mRNA. The trigger for gene silencing is double-stranded RNA (dsRNA) generated from an endogenous genomic locus or a foreign source, such as a transgene or virus. The process of gene silencing can be exploited in agriculture to control plant diseases and pests. Of the pests that impact crop yield (including nematodes, arthropods, rodents, snails, slugs and birds), insects constitute the largest and most diverse group. Here, we review the "pros" and "cons" of using RNAi technology mediated by dsRNA-expressing transgenic plants (host-induced gene silencing, HIGS) or direct application of chemically synthesized dsRNA to control plant-damaging insects. Rapid progress in elucidating RNAi mechanisms has led to the first commercial products on the market. Given the high potential of RNAi strategies, their use in agriculture, horticulture, and forestry will likely be extensive in the future. However, further studies are needed to improve the efficacy of RNAi-based plant protection strategies and to assess their associated safety risks.
Topics: Animals; Insect Control; Insecta; Plants, Genetically Modified; RNA Interference; RNA, Double-Stranded
PubMed: 31678220
DOI: 10.1016/j.biotechadv.2019.107463 -
Nature Communications Aug 2023Small interference RNAs are the key components of RNA interference, a conserved RNA silencing or viral defense mechanism in many eukaryotes. In Drosophila melanogaster,...
Small interference RNAs are the key components of RNA interference, a conserved RNA silencing or viral defense mechanism in many eukaryotes. In Drosophila melanogaster, Dicer-2 (DmDcr-2)-mediated RNAi pathway plays important roles in defending against viral infections and protecting genome integrity. During the maturation of siRNAs, two cofactors can regulate DmDcr-2's functions: Loqs-PD that is required for dsRNA processing, and R2D2 that is essential for the subsequent loading of siRNAs into effector Ago2 to form RISC complexes. However, due to the lack of structural information, it is still unclear whether R2D2 and Loqs-PD affect the functions of DmDcr-2 simultaneously. Here we present several cryo-EM structures of DmDcr-2/R2D2/Loqs-PD complex bound to dsRNAs with various lengths by the Helicase domain. These structures revealed that R2D2 and Loqs-PD can bind to different regions of DmDcr-2 without interfering with each other. Furthermore, the cryo-EM results demonstrate that these complexes can form large oligomers and assemble into fibers. The formation and depolymerization of these oligomers are associated with ATP hydrolysis. These findings provide insights into the structural mechanism of DmDcr-2 and its cofactors during siRNA processing.
Topics: Animals; DNA Helicases; Drosophila melanogaster; Drosophila Proteins; RNA Interference; RNA, Double-Stranded; RNA, Small Interfering; RNA-Binding Proteins
PubMed: 37633971
DOI: 10.1038/s41467-023-40919-1 -
Wiley Interdisciplinary Reviews. RNA Jul 2019Small RNAs and their associated RNA interference (RNAi) pathways underpin diverse mechanisms of gene regulation and genome defense across all three kingdoms of life and... (Review)
Review
Small RNAs and their associated RNA interference (RNAi) pathways underpin diverse mechanisms of gene regulation and genome defense across all three kingdoms of life and are integral to virus-host interactions. In plants, fungi and many animals, an ancestral RNAi pathway exists as a host defense mechanism whereby viral double-stranded RNA is processed to small RNAs that enable recognition and degradation of the virus. While this antiviral RNAi pathway is not generally thought to be present in mammals, other RNAi mechanisms can influence infection through both viral- and host-derived small RNAs. Furthermore, a burgeoning body of data suggests that small RNAs in mammals can function in a non-cell autonomous manner to play various roles in cell-to-cell communication and disease through their transport in extracellular vesicles. While vesicular small RNAs have not been proposed as an antiviral defense pathway per se, there is increasing evidence that the export of host- or viral-derived RNAs from infected cells can influence various aspects of the infection process. This review discusses the current knowledge of extracellular RNA functions in viral infection and the technical challenges surrounding this field of research. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action.
Topics: Eukaryotic Cells; Extracellular Vesicles; Gene Expression Regulation; Host Microbial Interactions; RNA Interference; RNA, Small Untranslated
PubMed: 30963709
DOI: 10.1002/wrna.1535 -
Yakugaku Zasshi : Journal of the... 2020RNA interference (RNAi) is the standard method of suppressing gene expression because of its target specificity, potency, and ability to silence the expression of... (Review)
Review
RNA interference (RNAi) is the standard method of suppressing gene expression because of its target specificity, potency, and ability to silence the expression of virtually any gene. Using 21-mer small interfering RNA (siRNA) is the general approach for inducing RNAi, as siRNA can be easily prepared using a DNA/RNA synthesizer. Synthetic siRNA can be chemically modified to increase the potency of RNAi activity and abrogate innate immune stimulation. However, designing chemically modified siRNA requires substantial experimentation. A practical method for understanding the interaction of siRNA and RNAi-related proteins and how modifications affect RNA-protein interactions is therefore needed. Plasmid DNA (pDNA) expressing short hairpin RNA (shRNA) can also be used to induce RNAi. pDNA produces numerous shRNAs that induce RNAi with potent and longterm RNAi activity, even if only one pDNA molecule is delivered to the nucleus. However, this approach has some drawbacks with regard to its therapeutic application, such as a low pDNA transfection efficiency due to its huge molecular size and innate immune responses induced by extra genes, such as CpG motifs. To overcome these issues with RNAi inducers (siRNA and pDNA), our group developed some chemical approaches using chemically modified oligonucleotides. This article focuses on our two original approaches. The first involves the groove modification of siRNA duplexes to understand siRNA-protein interactions using 7-bromo-7-deazaadenosine and 3-bromo-3-deazaadenosine as chemical probes, while the second involves the generation of RNAi medicine using chemically modified DNA, known as an intelligent shRNA expression device (iRed).
Topics: DNA; Drug Development; Immunity, Innate; Oligonucleotides; Protein Interaction Domains and Motifs; RNA Interference; RNA, Small Interfering; RNAi Therapeutics; Tubercidin
PubMed: 32999205
DOI: 10.1248/yakushi.20-00157 -
Advanced Healthcare Materials Jan 2017It has been nearly two decades since RNA-interference (RNAi) was first reported. While there are no approved clinical uses, several phase II and III clinical trials... (Review)
Review
It has been nearly two decades since RNA-interference (RNAi) was first reported. While there are no approved clinical uses, several phase II and III clinical trials suggest the great promise of RNAi therapeutics. One challenge for RNAi therapies is the controlled localization and sustained presentation to target tissues, to both overcome systemic toxicity concerns and to enhance in vivo efficacy. One approach that is emerging to address these limitations is the entrapment of RNAi molecules within hydrogels for local and sustained release. In these systems, nucleic acids are either delivered as siRNA conjugates or within nanoparticles. A plethora of hydrogels has been implemented using these approaches, including both traditional hydrogels that have already been developed for other applications and new hydrogels developed specifically for RNAi delivery. These hydrogels have been applied to various applications in vivo, including cancer, bone regeneration, inflammation and cardiac repair. This review will examine the design and implementation of such hydrogel RNAi systems and will cover the most recent applications of these systems.
Topics: Animals; Genetic Therapy; Humans; Hydrogels; RNA Interference; RNA, Small Interfering; Transfection
PubMed: 27976524
DOI: 10.1002/adhm.201601041 -
Cellular and Molecular Life Sciences :... Mar 2018RNA interference (RNAi) has been widely adopted to repress specific gene expression and is easily achieved by designing small interfering RNAs (siRNAs) with perfect... (Review)
Review
RNA interference (RNAi) has been widely adopted to repress specific gene expression and is easily achieved by designing small interfering RNAs (siRNAs) with perfect sequence complementarity to the intended target mRNAs. Although siRNAs direct Argonaute (Ago), a core component of the RNA-induced silencing complex (RISC), to recognize and silence target mRNAs, they also inevitably function as microRNAs (miRNAs) and suppress hundreds of off-targets. Such miRNA-like off-target repression is potentially detrimental, resulting in unwanted toxicity and phenotypes. Despite early recognition of the severity of miRNA-like off-target repression, this effect has often been overlooked because of difficulties in recognizing and avoiding off-targets. However, recent advances in genome-wide methods and knowledge of Ago-miRNA target interactions have set the stage for properly evaluating and controlling miRNA-like off-target repression. Here, we describe the intrinsic problems of miRNA-like off-target effects caused by canonical and noncanonical interactions. We particularly focus on various genome-wide approaches and chemical modifications for the evaluation and prevention of off-target repression to facilitate the use of RNAi with secured specificity.
Topics: Animals; Argonaute Proteins; Binding Sites; Gene Expression Regulation; Humans; MicroRNAs; RNA Interference; RNA, Small Interfering; RNA-Induced Silencing Complex
PubMed: 28905147
DOI: 10.1007/s00018-017-2656-0 -
Viruses Dec 2016Insects and other arthropods are the most important vectors of plant pathogens. The majority of plant pathogens are disseminated by arthropod vectors such as aphids,... (Review)
Review
Insects and other arthropods are the most important vectors of plant pathogens. The majority of plant pathogens are disseminated by arthropod vectors such as aphids, beetles, leafhoppers, planthoppers, thrips and whiteflies. Transmission of plant pathogens and the challenges in managing insect vectors due to insecticide resistance are factors that contribute to major food losses in agriculture. RNA interference (RNAi) was recently suggested as a promising strategy for controlling insect pests, including those that serve as important vectors for plant pathogens. The last decade has witnessed a dramatic increase in the functional analysis of insect genes, especially those whose silencing results in mortality or interference with pathogen transmission. The identification of such candidates poses a major challenge for increasing the role of RNAi in pest control. Another challenge is to understand the RNAi machinery in insect cells and whether components that were identified in other organisms are also present in insect. This review will focus on summarizing success cases in which RNAi was used for silencing genes in insect vector for plant pathogens, and will be particularly helpful for vector biologists.
Topics: Animals; Insect Vectors; Pest Control, Biological; RNA Interference
PubMed: 27973446
DOI: 10.3390/v8120329 -
RNA (New York, N.Y.) Apr 2015
Topics: Clustered Regularly Interspaced Short Palindromic Repeats; RNA; RNA Editing; RNA Interference
PubMed: 25780123
DOI: 10.1261/rna.050138.115 -
Theranostics 2021The approval of the first small interfering RNA (siRNA) drug Patisiran by FDA in 2018 marks a new era of RNA interference (RNAi) therapeutics. MicroRNAs (miRNA), an... (Review)
Review
The approval of the first small interfering RNA (siRNA) drug Patisiran by FDA in 2018 marks a new era of RNA interference (RNAi) therapeutics. MicroRNAs (miRNA), an important post-transcriptional gene regulator, are also the subject of both basic research and clinical trials. Both siRNA and miRNA mimics are ~21 nucleotides RNA duplexes inducing mRNA silencing. Given the well performance of siRNA, researchers ask whether miRNA mimics are unnecessary or developed siRNA technology can pave the way for the emergence of miRNA mimic drugs. Through comprehensive comparison of siRNA and miRNA, we focus on (1) the common features and lessons learnt from the success of siRNAs; (2) the unique characteristics of miRNA that potentially offer additional therapeutic advantages and opportunities; (3) key areas of ongoing research that will contribute to clinical application of miRNA mimics. In conclusion, miRNA mimics have unique properties and advantages which cannot be fully matched by siRNA in clinical applications. MiRNAs are endogenous molecules and the gene silencing effects of miRNA mimics can be regulated or buffered to ameliorate or eliminate off-target effects. An in-depth understanding of the differences between siRNA and miRNA mimics will facilitate the development of miRNA mimic drugs.
Topics: Animals; Biomimetic Materials; Biomimetics; Gene Expression Regulation; Gene Silencing; Humans; MicroRNAs; Molecular Mimicry; RNA Interference; RNA, Small Interfering
PubMed: 34522211
DOI: 10.7150/thno.62642