scholarly journals Exploring the functions of RNA interference pathway proteins: some functions are more RISCy than others?

2005 ◽  
Vol 387 (3) ◽  
pp. 561-571 ◽  
Author(s):  
Katarzyna JARONCZYK ◽  
Jon B. CARMICHAEL ◽  
Tom C. HOBMAN
Keyword(s):  
Rna Interference ◽  
Gene Silencing ◽  
Cell Cycle Regulators ◽  
Small Interfering Rnas ◽  
Piwi Domain ◽  
Therapeutic Technique ◽  
Silencing Pathways ◽  
Laboratory Tool ◽  
Molecular Therapeutic ◽  
Regulate Gene

PPD (PAZ Piwi domain) proteins and the Dicer family have been the subjects of intense study over the last 6 years. These proteins have well-established roles in RNAi (RNA interference), a process that relies on siRNAs (small interfering RNAs) or miRNAs (microRNAs) to mediate specificity. The development of techniques for applying RNAi as a laboratory tool and a molecular therapeutic technique has rapidly outpaced our understanding of the biology of this process. However, over the last 2 years, great strides have been made towards elucidating how PPD proteins and Dicer regulate gene-silencing at the pre- and post-transcriptional levels. In addition, evidence is beginning to emerge that suggests that these proteins have additional siRNA-independent roles as cell-cycle regulators. In the present review, we summarize the well-known roles of these two classes of proteins in gene-silencing pathways, as well as explore the evidence for novel roles of PPD and Dicer proteins.

scholarly journals Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A

2017 ◽  
Author(s):  
Shelby S Calkins ◽  
Nicole C Elledge ◽  
Stephen M. Marek ◽  
M B. Couger ◽  
Mostafa S Elshahed ◽  
...  
Keyword(s):  
Rna Interference ◽  
Gene Silencing ◽  
Neurospora Crassa ◽  
Dna Helicase ◽  
Small Interfering Rnas ◽  
Gene Encoding ◽  
Interacting Protein ◽  
Genes Encoding ◽  
Lactate Levels ◽  
Electron Sink

Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.

scholarly journals Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungusPecoramyces ruminantiumstrain C1A

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4276 ◽  
Author(s):  
Shelby S. Calkins ◽  
Nicole C. Elledge ◽  
Katherine E. Mueller ◽  
Stephen M. Marek ◽  
MB Couger ◽  
...  
Keyword(s):  
Rna Interference ◽  
Gene Silencing ◽  
Neurospora Crassa ◽  
Dna Helicase ◽  
Small Interfering Rnas ◽  
Gene Encoding ◽  
Interacting Protein ◽  
Genes Encoding ◽  
Lactate Levels ◽  
Electron Sink

Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungusPecoramyces ruminantiumstrain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute,Neurospora crassaQDE-3 homolog DNA helicase, Argonaute-interacting protein, andNeurospora crassaQIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lowerldhDtranscriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.

scholarly journals Cross-Kingdom Small RNAs Among Animals, Plants and Microbes

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 371 ◽  
Author(s):  
Zeng ◽  
Gupta ◽  
Jiang ◽  
Yang ◽  
Gong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Interference ◽  
Gene Silencing ◽  
Horizontal Transfer ◽  
Small Rnas ◽  
Signal Transmission ◽  
Fungal Diseases ◽  
Small Interfering Rnas ◽  
Eukaryotic Species ◽  
Non Coding Rnas

Small RNAs (sRNAs), a class of regulatory non-coding RNAs around 20~30-nt long, including small interfering RNAs (siRNAs) and microRNAs (miRNAs), are critical regulators of gene expression. Recently, accumulating evidence indicates that sRNAs can be transferred not only within cells and tissues of individual organisms, but also across different eukaryotic species, serving as a bond connecting the animal, plant, and microbial worlds. In this review, we summarize the results from recent studies on cross-kingdom sRNA communication. We not only review the horizontal transfer of sRNAs among animals, plants and microbes, but also discuss the mechanism of RNA interference (RNAi) signal transmission via cross-kingdom sRNAs. We also compare the advantages of host-induced gene silencing (HIGS) and spray-induced gene silencing (SIGS) technology and look forward to their applicable prospects in controlling fungal diseases.

scholarly journals Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A

2017 ◽  
Author(s):  
Shelby S Calkins ◽  
Nicole C Elledge ◽  
Stephen M. Marek ◽  
M B. Couger ◽  
Mostafa S Elshahed ◽  
...  
Keyword(s):  
Rna Interference ◽  
Gene Silencing ◽  
Neurospora Crassa ◽  
Dna Helicase ◽  
Small Interfering Rnas ◽  
Gene Encoding ◽  
Interacting Protein ◽  
Genes Encoding ◽  
Lactate Levels ◽  
Electron Sink

Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.

scholarly journals Chemical strategies for strand selection in short-interfering RNAs

RSC Advances ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 2415-2426
Author(s):  
Andrew J. Varley ◽  
Jean-Paul Desaulniers
Keyword(s):  
Rna Interference ◽  
Gene Silencing ◽  
Rnai Pathway ◽  
Specific Gene ◽  
Small Interfering Rnas ◽  
Chemical Strategies

Therapeutic small interfering RNAs (siRNAs) are double stranded RNAs capable of potent and specific gene silencing through activation of the RNA interference (RNAi) pathway.

RNA Interference-Mediated Gene Silencing of Pleiotrophin Through Polyethylenimine-Complexed Small Interfering RNAs In Vivo Exerts Antitumoral Effects in Glioblastoma Xenografts

2006 ◽  
Vol 0 (0) ◽  
pp. 060801084750001
Author(s):  
Marius Grzelinski ◽  
Beata Urban-Klein ◽  
Tobias Martens ◽  
Katrin Lamszus ◽  
Udo Bakowsky ◽  
...  
Keyword(s):  
Rna Interference ◽  
Gene Silencing ◽  
Small Interfering Rnas

scholarly journals Gene silencing by double stranded Ribonucleic acid (RNA)

2020 ◽  
Vol 5 (1) ◽  
pp. 41
Author(s):  
Hafiz Ghulam Muhu-Din Ahmed ◽  
Amna . ◽  
Shadab Shaukat ◽  
Iqra Kousar ◽  
Maria Rafiq ◽  
...  
Keyword(s):  
Rna Interference ◽  
Gene Silencing ◽  
Ribonucleic Acid ◽  
Rna Silencing ◽  
Defense Mechanism ◽  
Review Article ◽  
Transcriptional Gene Silencing ◽  
Post Transcriptional Gene Silencing ◽  
Silencing Pathways

Ribonucleic acid (RNA) silencing, RNA interference (RNAi) or post-transcriptional gene silencing takes place in a variety of eukaryotes and it was discovered firstly in the plants. The RNA silencing process is activated by a trigger from dsRNA predecessor. A very important step in the silencing pathways the conversion of dsRNA into small duplexes of RNA of the representative length and arrangement. Then these small dsRNA monitor RNA silencing by different mechanisms. Post transcriptional gene silencing mechanisms were initially identified as an anti-viral process that give protection to the organisms from the viruses or which inhibit the unsystematic incorporation of transposable components. The basic aim of this review article is to study the mechanism of gene silencing by dsRNA and the roles of certain proteins in cellular post transcriptional RNA silencing machinery and finally we also discuss the RNA silencing as an anti-viral defense mechanism in the plants. 

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