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New Advances in RNA Interference
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New Advances in RNA Interference

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 12770

Special Issue Editor

Dr. Tomer Ventura

E-Mail Website
Guest Editor
Centre for Bioinnovation, School of Science, Engineering and Technology, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
Interests: androgenic gland; aquaculture; crustaceans; disease management; gene silencing; genetic modification; monosex; selective breeding; sex reversal; yield improvement
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The discovery of RNA interference (RNAi) has led to a diverse array of applications across multiple industries, enabling a reverse genetic methodology across eukaryotes. The RNAi mechanism, which now has come to refer to the miRNA, siRNA, and piRNA pathways, has evolved many times in the course of eukaryotic evolution. Despite this, the mechanisms of RNAi have been perceived as uniform, and only in the last decade has research revealed intricacies in inter- and intraspecies mechanisms. The variation in silencing capacity between even closely related organisms and within populations has limited its potential applications, warranting greater fundamental research to better understand the RNAi mechanism. With the advent of -omics, this research is now feasible on a large scale and could benefit from incorporating multiple non-model organisms as a source for comparative analysis of the key components that enable effective gene silencing through RNAi. This Special Issue provides an over-arching look into the state of RNAi research, its mechanisms, applications, and prospects.

Dr. Tomer Ventura
Guest Editor

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Keywords

  • double stranded RNA
  • gene silencing
  • RNA binding peptides
  • RNA interference mechanism
  • short interfering RNA

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Published Papers (3 papers)

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Research

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16 pages, 2808 KiB  
Article
A Tale of Two Lobsters—Transcriptomic Analysis Reveals a Potential Gap in the RNA Interference Pathway in the Tropical Rock Lobster Panulirus ornatus
by Thomas M. Banks, Tianfang Wang, Quinn P. Fitzgibbon, Gregory G. Smith and Tomer Ventura
Int. J. Mol. Sci. 2022, 23(19), 11752; https://doi.org/10.3390/ijms231911752 - 4 Oct 2022
Cited by 4 | Viewed by 2490
Abstract
RNA interference (RNAi) has been widely utilised in many invertebrate models since its discovery, and in a majority of instances presents as a highly efficient and potent gene silencing mechanism. This is emphasized in crustaceans with almost all taxa having the capacity to [...] Read more.
RNA interference (RNAi) has been widely utilised in many invertebrate models since its discovery, and in a majority of instances presents as a highly efficient and potent gene silencing mechanism. This is emphasized in crustaceans with almost all taxa having the capacity to trigger effective silencing, with a notable exception in the spiny lobsters where repeated attempts at dsRNA induced RNAi have demonstrated extremely ineffective gene knockdown. A comparison of the core RNAi machinery in transcriptomic data from spiny lobsters (Panulirus ornatus) and the closely related slipper lobsters (Thenus australiensis, where silencing is highly effective) revealed that both lobsters possess all proteins involved in the small interfering and microRNA pathways, and that there was little difference at both the sequence and domain architecture level. Comparing the expression of these genes however demonstrated that T. australiensis had significantly higher expression in the transcripts encoding proteins which directly interact with dsRNA when compared to P. ornatus, validated via qPCR. These results suggest that low expression of the core RNAi genes may be hindering the silencing response in P. ornatus, and suggest that it may be critical to enhance the expression of these genes to induce efficient silencing in spiny lobsters. Full article
(This article belongs to the Special Issue New Advances in RNA Interference)
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10 pages, 2256 KiB  
Article
An RNA Interference Tool to Silence Genes in Sarcoptes scabiei Eggs
by Deepani D. Fernando, Pasi K. Korhonen, Robin B. Gasser and Katja Fischer
Int. J. Mol. Sci. 2022, 23(2), 873; https://doi.org/10.3390/ijms23020873 - 14 Jan 2022
Cited by 5 | Viewed by 1828
Abstract
In a quest for new interventions against scabies—a highly significant skin disease of mammals, caused by a parasitic mite Sarcoptes scabiei—we are focusing on finding new intervention targets. RNA interference (RNAi) could be an efficient functional genomics approach to identify such targets. [...] Read more.
In a quest for new interventions against scabies—a highly significant skin disease of mammals, caused by a parasitic mite Sarcoptes scabiei—we are focusing on finding new intervention targets. RNA interference (RNAi) could be an efficient functional genomics approach to identify such targets. The RNAi pathway is present in S. scabiei and operational in the female adult mite, but other developmental stages have not been assessed. Identifying potential intervention targets in the egg stage is particularly important because current treatments do not kill this latter stage. Here, we established an RNAi tool to silence single-copy genes in S. scabiei eggs. Using sodium hypochlorite pre-treatment, we succeeded in rendering the eggshell permeable to dsRNA without affecting larval hatching. We optimised the treatment of eggs with gene-specific dsRNAs to three single-copy target genes (designated Ss-Cof, Ss-Ddp, and Ss-Nan) which significantly and repeatedly suppressed transcription by ~66.6%, 74.3%, and 84.1%, respectively. Although no phenotypic alterations were detected in dsRNA-treated eggs for Ss-Cof and Ss-Nan, the silencing of Ss-Ddp resulted in a 38% reduction of larval hatching. This RNAi method is expected to provide a useful tool for larger-scale functional genomic investigations for the identification of essential genes as potential drug targets. Full article
(This article belongs to the Special Issue New Advances in RNA Interference)
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Review

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15 pages, 848 KiB  
Review
RNAi Crop Protection Advances
by Alejandro Hernández-Soto and Randall Chacón-Cerdas
Int. J. Mol. Sci. 2021, 22(22), 12148; https://doi.org/10.3390/ijms222212148 - 10 Nov 2021
Cited by 47 | Viewed by 7785
Abstract
RNAi technology is a versatile, effective, safe, and eco-friendly alternative for crop protection. There is plenty of evidence of its use through host-induced gene silencing (HIGS) and emerging evidence that spray-induced gene silencing (SIGS) techniques can work as well to control viruses, bacteria, [...] Read more.
RNAi technology is a versatile, effective, safe, and eco-friendly alternative for crop protection. There is plenty of evidence of its use through host-induced gene silencing (HIGS) and emerging evidence that spray-induced gene silencing (SIGS) techniques can work as well to control viruses, bacteria, fungi, insects, and nematodes. For SIGS, its most significant challenge is achieving stability and avoiding premature degradation of RNAi in the environment or during its absorption by the target organism. One alternative is encapsulation in liposomes, virus-like particles, polyplex nanoparticles, and bioclay, which can be obtained through the recombinant production of RNAi in vectors, transgenesis, and micro/nanoencapsulation. The materials must be safe, biodegradable, and stable in multiple chemical environments, favoring the controlled release of RNAi. Most of the current research on encapsulated RNAi focuses primarily on oral delivery to control insects by silencing essential genes. The regulation of RNAi technology focuses on risk assessment using different approaches; however, this technology has positive economic, environmental, and human health implications for its use in agriculture. The emergence of alternatives combining RNAi gene silencing with the induction of resistance in crops by elicitation and metabolic control is expected, as well as multiple silencing and biotechnological optimization of its large-scale production. Full article
(This article belongs to the Special Issue New Advances in RNA Interference)
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