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

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.

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.

scholarly journals RNA Interference Is Enhanced by Knockdown of Double-Stranded RNases in the Yellow Fever Mosquito Aedes aegypti

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 327 ◽  
Author(s):  
David Giesbrecht ◽  
Daniel Heschuk ◽  
Ian Wiens ◽  
David Boguski ◽  
Parker LaChance ◽  
...  
Keyword(s):  
Rna Interference ◽  
Aedes Aegypti ◽  
Fluorescent Protein ◽  
Mosquito Control ◽  
Ex Vivo ◽  
Double Stranded Rna ◽  
Industry Standards ◽  
Rna Targeting ◽  
Aegypti Genome ◽  
Control Technologies

RNA interference (RNAi) techniques are being developed for a range of pest insect control technologies, including the sterile insect technique (SIT) and double-stranded RNA (dsRNA)-based insecticides. In SIT applications, where >99% of the released males should be sterile to meet industry standards, the efficiency of RNAi will need to be improved for many insect species if this technology is to be adopted. Endogenous dsRNases can impede dsRNA delivery in some insects, and, here, we investigated whether dsRNases in the midgut could limit RNAi efficacy in the mosquito Aedes aegypti. Ten putative dsRNases were identified in the Ae. aegypti genome, with two highly expressed in the midguts of larvae. Using an ex vivo assay, we observed that dsRNA was rapidly degraded within the mosquito larva’s gut. Double-stranded RNA targeting these two dsRNases, when fed to the larvae, effectively reduced gut dsRNase activity. When these dsRNase-specific dsRNAs were co-delivered with dsRNA targeting a cyan fluorescent protein (CFP) reporter gene, greater knockdown of CFP fluorescence was observed. These results suggest that inhibiting dsRNase activity could enable the implementation of RNAi-based mosquito control methods.

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 Inactivation of the type I interferon pathway reveals long double‐stranded RNA ‐mediated RNA interference in mammalian cells

2016 ◽  
Vol 35 (23) ◽  
pp. 2505-2518 ◽  
Author(s):  
Pierre V Maillard ◽  
Annemarthe G Van der Veen ◽  
Safia Deddouche‐Grass ◽  
Neil C Rogers ◽  
Andres Merits ◽  
...  
Keyword(s):  
Rna Interference ◽  
Mammalian Cells ◽  
Type I Interferon ◽  
Type I ◽  
Double Stranded Rna ◽  
Interferon Pathway
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