siRNA Specificity: RNAi Mechanisms and Strategies to Reduce Off-Target Effects

Neumeier, Julia; Meister, Gunter

doi:10.3389/fpls.2020.526455

Cited by 83 publications

(62 citation statements)

References 87 publications

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“…We have previously reported a similar variation in phenotypic strength after knockdown with multiple RNAi hairpins targeting other RBPs, notably SF1 , Hrb87F , snf , Prp19 , and others ( Kao et al, 2021 ). These results illustrate the experimental importance of testing multiple, independent RNAi constructs to distinguish hypomorphic from null phenotypes, beyond merely addressing off-target effects ( Mohr & Perrimon, 2012 ; Kaya-Çopur & Schnorrer, 2019 ; Neumeier & Meister, 2020 ). Moreover, tuning the level of knockdown can offer insight into regulatory events that are sensitive to RBP activity level.…”

Section: Discussionmentioning

confidence: 80%

Rbfox1 is required for myofibril development and maintaining fiber type–specific isoform expression in Drosophila muscles

et al. 2022

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Protein isoform transitions confer muscle fibers with distinct properties and are regulated by differential transcription and alternative splicing. RNA-binding Fox protein 1 (Rbfox1) can affect both transcript levels and splicing, and is known to contribute to normal muscle development and physiology in vertebrates, although the detailed mechanisms remain obscure. In this study, we report that Rbfox1 contributes to the generation of adult muscle diversity in Drosophila. Rbfox1 is differentially expressed among muscle fiber types, and RNAi knockdown causes a hypercontraction phenotype that leads to behavioral and eclosion defects. Misregulation of fiber type–specific gene and splice isoform expression, notably loss of an indirect flight muscle–specific isoform of Troponin-I that is critical for regulating myosin activity, leads to structural defects. We further show that Rbfox1 directly binds the 3′-UTR of target transcripts, regulates the expression level of myogenic transcription factors myocyte enhancer factor 2 and Salm, and both modulates expression of and genetically interacts with the CELF family RNA-binding protein Bruno1 (Bru1). Rbfox1 and Bru1 co-regulate fiber type–specific alternative splicing of structural genes, indicating that regulatory interactions between FOX and CELF family RNA-binding proteins are conserved in fly muscle. Rbfox1 thus affects muscle development by regulating fiber type–specific splicing and expression dynamics of identity genes and structural proteins.

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Section: Discussionmentioning

confidence: 80%

Rbfox1 is required for myofibril development and maintaining fiber type–specific isoform expression in Drosophila muscles

et al. 2022

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“…In coleopterans, an orally delivered long dsRNA (≥200-500 nucleotides) is processed into the cell to yield siRNAs, which ultimately trigger mRNA degradation [66]. The dsRNA fragment size may be reduced to avoid off-target silencing [68,69]. In addition, protection by nanoparticles increased the efficiency of RNAi action in Euchistos heros [66].…”

Section: Dsrna Stability and Efficiencymentioning

confidence: 99%

“…Nonetheless, these nanoparticle-based RNA pesticides must be simple and the required raw materials should be affordable for low-cost production [61,70]. In addition, application dsRNA-based pesticides through either irrigation or foliar spray must be explored [68] to promote their oral uptake by insects via feeding [15].…”

Section: Dsrna Stability and Efficiencymentioning

confidence: 99%

Advances and Challenges in RNA Interference Technology for Citrus Huanglongbing Vector Control

Marques¹,

Angelotti-Mendonça

Roberto

2021

Horticulturae

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Citrus species, including sweet oranges, grapefruits, pomelos, and lemons, are the most widely cultivated trees and consumed fruits worldwide. In citrus orchard management, the control of Huanglongbing (HLB) disease and its insect vector Diaphorina citri (Asian citrus psyllid, ACP) represents a major global challenge. Consumers have been increasingly pushing the citrus production chain toward a more sustainable system, including stringent measures to prevent the use of chemical pesticides. In recent years, biotechnological advances have offered safe and environmentally friendly alternatives for crop production. Technologies such as RNA interference (RNAi)-mediated gene silencing have emerged as innovative tools for agricultural pest management. Here, we provide an overview of RNAi as a promising approach for ACP control and discuss the associated challenges. Despite the availability of specific silencing sequences aimed at a target gene of the insect pest, the uptake of double-stranded RNA is limited in hemipteran insects. In this context, improved delivery methods, stability maintenance, and RNAi response are considered the factors contributing to the increased effectiveness of exogenous RNAi against hemipteran pests. These approaches can serve as potential tools for efficient ACP control.

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“…Castellanos et al [31] reported that the combined use of RNAi-mediated gene silencing against the Neotropical brown stink bug Euschistus heros (F.) (Hemiptera, Pentatomidae), together with eggs of the parasitoid Telenomus podisi Ashmead (Hymenoptera, Scelionidae), proved to be a feasible approach. In RNAi-mediated pest control, off-target effects need to be analysed before its implemen-tation [32,33]. In a study by Pan et al [28], the effects of dietary RNAi toxicity assay of Diabrotica virgifera virgifera LeConte (Coleoptera, Chrysomelidae) active dsRNA for the gene V-ATPase proved to be detrimental to four non-target ladybird species (Coleoptera, Coccinellidae).…”

Section: Introductionmentioning

confidence: 99%

dsRNA-Mediated Pest Management of Tuta absoluta Is Compatible with Its Biological Control Agent Nesidiocoris tenuis

Sarmah

Kaldis

Taning

et al. 2021

Insects

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RNAi-mediated insect pest management has recently shown promising results against the most serious pest of tomato, the tomato leafminer, Tuta absoluta. This study aimed to investigate whether dsRNA (dsTa-αCOP) designed to target the T. absoluta-αCOP gene could cause adverse effects to its biocontrol agent, the mirid predator, Nesidiocoris tenuis. Oral exposure of N. tenuis to dsRNA (dsNt-αCOP) designed to target N. tenuis-αCOP resulted in a 61%, 67% and 55% reduction in its transcript level in comparison to the sucrose, dsGFP and dsTa-αCOP treatments, respectively. In addition, significantly higher mortality of 57% was recorded in dsNt-αCOP-treated N. tenuis when compared to the sucrose (7%), dsGFP (10%) and dsTa-αCOP (10%) treatments. Moreover, the predation rate of ~33–39 Ephestia kuehniella eggs per N. tenuis adult dramatically reduced to almost half in the surviving dsNt-αCOP-treated N. tenuis. This worst-case exposure scenario confirmed for the first time that the RNAi machinery is functional in this species and that the risk of exposure through the oral route is possible. In contrast, dsTa-αCOP did not cause any sub-lethal effects to N. tenuis upon oral exposure. Oral exposure of T. absoluta to dsTa-αCOP resulted in 50% mortality. In the context of a biosafety risk assessment of RNAi-mediated insect management, investigating the effects on non-target organisms is essential in order to include this method as part of an integrated pest management strategy. Based on our laboratory assays, RNAi-mediated control is compatible with the biological control of T. absoluta by its natural enemy N. tenuis, adding the RNAi approach in the armoire of integrated pest management of T. absoluta.

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siRNA Specificity: RNAi Mechanisms and Strategies to Reduce Off-Target Effects

Cited by 83 publications

References 87 publications

Rbfox1 is required for myofibril development and maintaining fiber type–specific isoform expression in Drosophila muscles

Rbfox1 is required for myofibril development and maintaining fiber type–specific isoform expression in Drosophila muscles

Advances and Challenges in RNA Interference Technology for Citrus Huanglongbing Vector Control

dsRNA-Mediated Pest Management of Tuta absoluta Is Compatible with Its Biological Control Agent Nesidiocoris tenuis

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