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

2021 ◽  
Vol 11 ◽  
Author(s):  
Julia Neumeier ◽  
Gunter Meister
Keyword(s):  
Rna Interference ◽  
Protein A ◽  
Crop Protection ◽  
Protein Family ◽  
Argonaute Protein ◽  
Guide Strand ◽  
Rna Modifications ◽  
Double Stranded Rna ◽  
Target Rna ◽  
Target Effects

Short interfering RNAs (siRNAs) are processed from long double-stranded RNA (dsRNA), and a guide strand is selected and incorporated into the RNA-induced silencing complex (RISC). Within RISC, a member of the Argonaute protein family directly binds the guide strand and the siRNA guides RISC to fully complementary sites on-target RNAs, which are then sequence-specifically cleaved by the Argonaute protein—a process commonly referred to as RNA interference (RNAi). In animals, endogenous microRNAs (miRNAs) function similarly but do not lead to direct cleavage of the target RNA but to translational inhibition followed by exonucleolytic decay. This is due to only partial complementarity between the miRNA and the target RNA. SiRNAs, however, can function as miRNAs, and partial complementarity can lead to miRNA-like off-target effects in RNAi applications. Since siRNAs are widely used not only for screening but also for therapeutics as well as crop protection purposes, such miRNA-like off-target effects need to be minimized. Strategies such as RNA modifications or pooling of siRNAs have been developed and are used to reduce off-target effects.

scholarly journals Non-Target Effects of Green Fluorescent Protein (GFP)-Derived Double-Stranded RNA (dsRNA-GFP) Used in Honey Bee RNA Interference (RNAi) Assays

Insects ◽  
2013 ◽  
Vol 4 (1) ◽  
pp. 90-103 ◽  
Author(s):  
Francis Nunes ◽  
Aline Aleixo ◽  
Angel Barchuk ◽  
Ana Bomtorin ◽  
Christina Grozinger ◽  
...  
Keyword(s):  
Green Fluorescent Protein ◽  
Rna Interference ◽  
Honey Bee ◽  
Fluorescent Protein ◽  
Double Stranded Rna ◽  
Green Fluorescent ◽  
Target Effects

scholarly journals Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1187
Author(s):  
Michael Wassenegger ◽  
Athanasios Dalakouras
Keyword(s):  
Dna Methylation ◽  
Rna Interference ◽  
Gene Silencing ◽  
Plant Cells ◽  
Transcriptional Gene Silencing ◽  
Rnai Machinery ◽  
Double Stranded Rna ◽  
Post Transcriptional Gene Silencing ◽  
Cumulative Amount

Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene Silencing (PTGS) and RNA-directed DNA Methylation (RdDM), and the latter has the potential to trigger Transcriptional Gene Silencing (TGS). Over the last three decades, the employment of viroid-based systems has immensely contributed to our understanding of both of these RNAi facets. In this review, we highlight the role of Pospiviroidae in the discovery of RdDM, expound the gradual elucidation through the years of the diverse array of RdDM’s mechanistic details and propose a revised RdDM model based on the cumulative amount of evidence from viroid and non-viroid systems.

scholarly journals Analysis of maxillopedia Expression Pattern and Larval Cuticular Phenotype in Wild-Type and Mutant Tribolium

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 721-731 ◽  
Author(s):  
Teresa D Shippy ◽  
Jianhua Guo ◽  
Susan J Brown ◽  
Richard W Beeman ◽  
Robin E Denell
Keyword(s):  
Rna Interference ◽  
Expression Pattern ◽  
Tribolium Castaneum ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Homeotic Gene ◽  
Wild Type ◽  
Double Stranded Rna ◽  
Similar Expression ◽  
Mutant Phenotypes

Abstract The Tribolium castaneum homeotic gene maxillopedia (mxp) is the ortholog of Drosophila proboscipedia (pb). Here we describe and classify available mxp alleles. Larvae lacking all mxp function die soon after hatching, exhibiting strong transformations of maxillary and labial palps to legs. Hypomorphic mxp alleles produce less severe transformations to leg. RNA interference with maxillopedia double-stranded RNA results in phenocopies of mxp mutant phenotypes ranging from partial to complete transformations. A number of gain-of-function (GOF) mxp alleles have been isolated based on transformations of adult antennae and/or legs toward palps. Finally, we have characterized the mxp expression pattern in wild-type and mutant embryos. In normal embryos, mxp is expressed in the maxillary and labial segments, whereas ectopic expression is observed in some GOF variants. Although mxp and Pb display very similar expression patterns, pb null embryos develop normally. The mxp mutant larval phenotype in Tribolium is consistent with the hypothesis that an ancestral pb-like gene had an embryonic function that was lost in the lineage leading to Drosophila.

scholarly journals The Argonaute protein family

2008 ◽  
Vol 9 (2) ◽  
pp. 210 ◽  
Author(s):  
Julia Höck ◽  
Gunter Meister
Keyword(s):  
Protein Family ◽  
Argonaute Protein

scholarly journals dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference

2005 ◽  
Vol 33 (Web Server) ◽  
pp. W589-W591 ◽  
Author(s):  
Y. Naito ◽  
T. Yamada ◽  
T. Matsumiya ◽  
K. Ui-Tei ◽  
K. Saigo ◽  
...  
Keyword(s):  
Rna Interference ◽  
Target Search ◽  
Double Stranded Rna ◽  
Highly Sensitive

Selective reduction of dormant maternal mRNAs in mouse oocytes by RNA interference

Development ◽  
2000 ◽  
Vol 127 (19) ◽  
pp. 4147-4156 ◽  
Author(s):  
P. Svoboda ◽  
P. Stein ◽  
H. Hayashi ◽  
R.M. Schultz
Keyword(s):  
Rna Interference ◽  
Map Kinase ◽  
Selective Reduction ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Double Stranded Rna ◽  
Mouse Oocytes ◽  
Tissue Plasminogen ◽  
Maternal Mrnas ◽  
Specific Mrna

Specific mRNA degradation mediated by double-stranded RNA (dsRNA), which is termed RNA interference (RNAi), is a useful tool with which to study gene function in several systems. We report here that in mouse oocytes, RNAi provides a suitable and robust approach to study the function of dormant maternal mRNAs. Mos (originally known as c-mos) and tissue plasminogen activator (tPA, Plat) mRNAs are dormant maternal mRNAs that are recruited during oocyte maturation; translation of Mos mRNA results in the activation of MAP kinase. dsRNA directed towards Mos or Plat mRNAs in mouse oocytes effectively results in the specific reduction of the targeted mRNA in both a time- and concentration-dependent manner. Moreover, dsRNA is more potent than either sense or antisense RNAs. Targeting the Mos mRNA results in inhibiting the appearance of MAP kinase activity and can result in parthenogenetic activation. Mos dsRNA, therefore, faithfully phenocopies the Mos null mutant. Targeting the Plat mRNA with Plat dsRNA results in inhibiting production of tPA activity. Finally, effective reduction of the Mos and Plat mRNA is observed with stoichiometric amounts of Mos and Plat dsRNA, respectively.

The economics of RNAi-based innovation: from the innovation landscape to consumer acceptance.

2021 ◽  
pp. 159-166
Author(s):  
Vera Ventura ◽  
Dario G. Frisio
Keyword(s):  
Rna Interference ◽  
Gene Silencing ◽  
Crop Protection ◽  
Consumer Perceptions ◽  
Market Potential ◽  
Consumer Acceptance ◽  
Innovative Technology ◽  
Sustainable Solutions

Abstract RNA interference (RNAi) is an innovative technology of gene silencing which offers great opportunities for the development of sustainable solutions for crop protection. This chapter discusses the market potential of RNAi innovation, the application of RNAi for biocontrol, and stakeholder and consumer perceptions of RNAi technologies.

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