RNA interference: listening to the sound of silence

Fem-1 Gene of Chinese White Pine Beetle (Dendroctonus armandi): Function and Response to Environmental Treatments

Dendroctonus armandi (Tsai and Li) (Coleoptera: Curculionidae: Scolytinae) is regarded as the most destructive forest pest in the Qinling and Bashan Mountains of China. The sex determination of Dendroctonus armandi plays a significant role in the reproduction of its population. In recent years, the role of the fem-1 gene in sex determination in other insects has been reported. However, the function and expression of the fem-1 gene in Dendroctonus armandi remain uncertain. In this study, three fem-1 genes were cloned and characterized. These were named Dafem-1A, Dafem-1B, and Dafem-1C, respectively. The expression levels of these three Dafem-1 genes vary at different stages of development and between the sexes. In response to different environmental treatments, including temperature, nutrients, terpenoids, and feeding duration, significant differences were observed between the three Dafem-1 genes at different developmental stages and between males and females. Furthermore, injection of double-stranded RNA (dsRNA) targeting the expressions of the Dafem-1A, Dafem-1B, and Dafem-1C genes resulted in increased mortality, deformity, and decreased emergence rates, as well as an imbalance in the sex ratio. Following the interference with Dafem-1A and Dafem-1C, no notable difference was observed in the expression of the Dafem-1B gene. Similarly, after the interference with the Dafem-1B gene, no significant difference was evident in the expression levels of the Dafem-1A and Dafem-1C genes. However, the interference of either the Dafem-1A or Dafem-1C gene results in the downregulation of the other gene. The aforementioned results demonstrate that the Dafem-1A, Dafem-1B, and Dafem-1C genes play a pivotal role in the regulation of life development and sex determination. Furthermore, it can be concluded that external factors such as temperature, nutrition, terpenoids, and feeding have a significant impact on the expression levels of the Dafem-1A, Dafem-1B, and Dafem-1C genes. This provides a crucial theoretical foundation for further elucidating the sex determination mechanism of Dendroctonus armandi.

An introduction to RNA therapeutics and their potentials

RNA therapeutics is a biological term regarding the usage of RNA-based molecules for medical purposes. Thanks to the success of mRNA-vaccine production against COVID-19, RNA therapeutics has gained more and more attention and investigation from worldwide scientists. It is considered as one of the promising alternatives for conventional drugs. In this first chapter, we presented an overview of the history and perspectives of RNA therapeutics' development. This chapter also explained the underlying mechanisms of different RNA-based molecules, including antisense oligonucleotide, interfering RNA (iRNA), aptamer, and mRNA, from degrading mRNA to inactivating targeted protein. Although there are many advantages of RNA therapeutics, its challenges in designing RNA chemical structure and the delivery vehicle need to be discussed. We described advanced technologies in the development of drug delivery systems that are positively correlated to the efficacy of the drug. Our aim is to provide a general background of RNA therapeutics to the audience before introducing plenty of more detailed parts, including clinical applications in certain diseases in the following chapters of the "RNA therapeutics" book.

Fluorescent Nanoparticle-RNAi-Mediated Silencing of Sterol Carrier Protein-2 Gene Expression Suppresses the Growth, Development, and Reproduction of Helicoverpa armigera

Helicoverpa armigera is a polyphagous destructive lepidopteran pest with strong Bacillus thuringiensis (Bt) resistance. Cholesterol, a vital component for insect growth, can only be obtained from food, and its transfer and metabolism are regulated by sterol carrier protein-2 (SCP-2). This study examined whether H. armigera SCP-2 (HaSCP-2) gene expression, involved in cholesterol absorption, can be silenced by nanocarrier fluorescent nanoparticle-RNA interference (FNP-RNAi) by larval feeding and whether the silencing affected H. armigera development. Fluorescence microscopy showed that nanoparticle-siRNA was distributed in Ha cells and the larval midgut. FNP-HaSCP-2 siRNA suppressed HaSCP-2 expression by 52.5% in H.armigera Ha cells. FNP can effectively help deliver siRNA into cells, protect siRNA, and is not affected by serum. FNP-siRNA in vivo biological assays showed that HaSCP-2 transcript levels were inhibited by 70.19%, 68.16%, and 67.66% in 3rd, 4th, and 5th instar larvae, leading to a decrease in the cholesterol level in the larval and prepupal fatbodies. The pupation rate and adult emergence were reduced to 26.0% and 56.52%, respectively. This study demonstrated that FNP could deliver siRNA to cells and improve siRNA knockdown efficiency. HaSCP-2 knockdown by FNP-siRNA in vivo hindered H. armigera growth and development. FNP could enhance RNAi efficiency to achieve pest control by SCP-2-targeted FNP-RNAi.

Star Polycation Mediated dsRNA Improves the Efficiency of RNA Interference in Phytoseiulus persimilis

RNA interference (RNAi) is one of the most widely used techniques to study gene functions. There is still a lack of RNAi techniques that can be applied in Phytoseiidae conveniently and efficiently. Star Polycation is a new nanomaterial commonly used as a carrier of dsRNA in RNAi. Five genes of P. persimilis (PpATPb, PpATPd, PpRpL11, PpRpS2, and Pptra-2) were selected to verify whether SPc promotes the delivery of dsRNA into P. persimilis through soaking. When each of the five genes were interfered using SPc-mediated dsRNA, the total number of success offspring produced per female in six days decreased by ca. 92%, 92%, 91%, 96%, and 64%. When PpATPb, PpATPd, PpRpL11, or PpRpS2 was interfered, both the fecundity and egg hatching rate decreased. In contrast, when Pptra-2 was interfered, reduction in the reproductive capability was mainly the result of the decreased egg hatching rate. Correspondingly, when the target gene was interfered, P. persimilis expression of PpRpL11 reduced by 63.95%, while that of the other four genes reduced by at least 80%. Our studies showed that nanomaterials, such as SPc, have the potential to be used in RNA interference of phytoseiid mites.

Chemical engineering of therapeutic siRNAs for allele-specific gene silencing in Huntington's disease models

Small interfering RNAs are a new class of drugs, exhibiting sequence-driven, potent, and sustained silencing of gene expression in vivo. We recently demonstrated that siRNA chemical architectures can be optimized to provide efficient delivery to the CNS, enabling development of CNS-targeted therapeutics. Many genetically-defined neurodegenerative disorders are dominant, favoring selective silencing of the mutant allele. In some cases, successfully targeting the mutant allele requires targeting single nucleotide polymorphism (SNP) heterozygosities. Here, we use Huntington’s disease (HD) as a model. The optimized compound exhibits selective silencing of mutant huntingtin protein in patient-derived cells and throughout the HD mouse brain, demonstrating SNP-based allele-specific RNAi silencing of gene expression in vivo in the CNS. Targeting a disease-causing allele using RNAi-based therapies could be helpful in a range of dominant CNS disorders where maintaining wild-type expression is essential.

Chemically modified siRNAs distinguish between mutant and normal huntingtin based on a single nucleotide difference and lower mutant huntingtin specifically in patient derived cells and in a mouse model of Huntington’s disease.

Novel molecular approaches to combat vectors and vector-borne viruses: Special focus on RNA interference (RNAi) mechanisms

Vector-borne diseases, such as dengue, chikungunya, zika, yellow fever etc pose significant burden among the infectious diseases globally, especially in tropical and sub-tropical regions. Globalization, deforestation, urbanization, climate change, uncontrolled population growth, inadequate waste management and poor vector-management infrastructure have all contributed to the expansion of vector habitats and subsequent increase in vector-borne diseases throughout the world. Conventional vector control methods, such as use of insecticides, have significant negative environmental repercussions in addition to developing resistance in vectors. Till date, a very few vaccines or antiviral therapies have been approved for the treatment of vector borne diseases. In this review, we have discussed emerging molecular approaches like CRISPR (clustered regularly interspaced short palindromic repeats)/Cas-9, sterile insect technique (SIT), release of insects carrying a dominant lethal (RIDL), Wolbachia (virus transmission blocking) and RNA interference (RNAi) to combat vector and vector-borne viruses. Due to the extensive advancements in RNAi research, a special focus has been given on its types, biogenesis, mechanism of action, delivery and experimental studies evaluating their application as anti-mosquito and anti-viral agent. These technologies appear to be highly promising in terms of contributing to vector control and antiviral drug development, and hence can be used to reduce global vector and vector-borne disease burden.

Feasibility of Systemically Applied dsRNAs for Pest-Specific RNAi-Induced Gene Silencing in White Oak

The efficacy of double-stranded RNA (dsRNA) in inducing host specific gene knockdown and mortality has been demonstrated in a multitude of insects and dsRNAs are being integrated for pest suppression in a variety of agricultural and horticultural crops. However, less attention has been applied to their use in forest settings, despite the demonstrated susceptibility of multiple forest pests to RNAi. Prior to implementation for forest pest suppression, characterization of the specificity, efficacy, and behavior of dsRNAs in the environment is essential. Therefore, we investigated the translocation and retention of exogenously applied dsRNA in an economically and ecologically significant hardwood tree when applied hydroponically. White oak (Quercus alba, L.) seedlings were exposed to dsRNAs as a root soak, and at 1, 3, 5, and 7 days post-exposure were destructively sampled, divided into stem and leaf tissue, and the RNA extracted. Gel electrophoresis was used to visualize the presence of exogenous dsRNA in treated seedling material and Sanger sequencing was used to further verify recovery of treatment dsRNAs. Both techniques confirmed the presence of the exogenously applied dsRNAs in each tissue type at each sample interval, demonstrating successful uptake and translocation of dsRNAs through white oak tissues. Our findings support root uptake as a viable delivery method for dsRNAs in hardwood seedlings, which could provide single tree protection from selected tree feeding pests or pathogens.

An RNAi therapeutic targeting hepatic DGAT2 in a genetically obese mouse model of nonalcoholic steatohepatitis

Nonalcoholic steatohepatitis (NASH) is a severe liver disorder characterized by triglyceride accumulation, severe inflammation, and fibrosis. With the recent increase in prevalence, NASH is now the leading cause of liver transplant, with no approved therapeutics available. Although the exact molecular mechanism of NASH progression is not well understood, a widely held hypothesis is that fat accumulation is the primary driver of the disease. Therefore, diacylglycerol O-acyltransferase 2 (DGAT2), a key enzyme in triglyceride synthesis, has been explored as a NASH target. RNAi-based therapeutics is revolutionizing the treatment of liver diseases, with recent chemical advances supporting long-term gene silencing with single subcutaneous administration. Here, we identified a hyper-functional, fully chemically stabilized GalNAc-conjugated small interfering RNA (siRNA) targeting DGAT2 (Dgat2-1473) that, upon injection, elicits up to 3 months of DGAT2 silencing (>80%-90%, p < 0.0001) in wild-type and NSG-PiZ "humanized" mice. Using an obesity-driven mouse model of NASH (ob/ob-GAN), Dgat2-1473 administration prevents and reverses triglyceride accumulation (>85%, p < 0.0001) without increased accumulation of diglycerides, resulting in significant improvement of the fatty liver phenotype. However, surprisingly, the reduction in liver fat did not translate into a similar impact on inflammation and fibrosis. Thus, while Dgat2-1473 is a practical, long-lasting silencing agent for potential therapeutic attenuation of liver steatosis, combinatorial targeting of a second pathway may be necessary for therapeutic efficacy against NASH.

Functional Characterization of Allatostatin C (PISCF/AST) and Juvenile Hormone Acid O-Methyltransferase in Dendroctonus armandi

Allatostatin C (PISCF/AST) is a neuropeptide gene that affects juvenile hormone (JH) synthesis in the corpora allata. Juvenile hormone acid O-methyltransferase (JHAMT) is a key gene in the JH biosynthetic pathway. In this study, two genes encoding DaAST and DaJHAMT were cloned. Both DaAST and DaJHAMT were expressed in the larvae, pupae and adults of Chinese white pine beetle (Dendroctonus armandi), and highly expressed in the head and the gut. The expression of the two genes was induced by JH analog (JHA) methoprene and the functions of the two genes were then investigated by RNAi. Considering the role of hormones in metamorphosis, JHA significantly induced DaAST and DaJHAMT in the larval stage. DaAST knockdown in larvae, pupae and adults significantly increased the DaJHAMT mRNA levels. Moreover, knockdown of DaAST instead of DaJHAMT increased pupae mortality and the abnormal rate of emergence morphology and reduced emergence rates. However, knockdown of DaJHAMT instead of DaAST significantly reduced frontalin biosynthesis in adult males. The results showed that DaAST acts as an allatostatin and inhibits JH biosynthesis, and that JHAMT is a key regulatory enzyme for JH synthesis in the D. armandi.

Pharmaceutical applications of framework nucleic acids

DNA is a biological polymer that encodes and stores genetic information in all living organism. Particularly, the precise nucleobase pairing inside DNA is exploited for the self-assembling of nanostructures with defined size, shape and functionality. These DNA nanostructures are known as framework nucleic acids (FNAs) for their skeleton-like features. Recently, FNAs have been explored in various fields ranging from physics, chemistry to biology. In this review, we mainly focus on the recent progress of FNAs in a pharmaceutical perspective. We summarize the advantages and applications of FNAs for drug discovery, drug delivery and drug analysis. We further discuss the drawbacks of FNAs and provide an outlook on the pharmaceutical research direction of FNAs in the future.

Application of the RNA interference technique to Xenopus embryos: Specific reduction of the β-catenin gene products by short double-stranded RNA produced by recombinant human Dicer

RNA interference (RNAi) is a technique for suppressing the function of specific genes and is widely used in many organisms, including yeast, nematodes, flies, plants, mice, and cultured mammalian cells. As of date, this technique has not been successfully applied to Xenopus laevis embryos. In this study, we applied RNAi to Xenopus embryos using β-catenin as a model gene. Injection of long double-stranded RNA (dsRNA) corresponding to the 3'-untranslated region of β-catenin mRNA into embryos induced embryonic lethality without any specific phenotype. However, injection of short dsRNA, generated from long dsRNA by treatment with recombinant human Dicer, into embryos resulted in decreased expression of endogenous β-catenin mRNA and protein, as well as decreased Wnt signaling activity in the embryos. The decrease in β-catenin mRNA and protein levels was observed only after mid-blastula transition. Embryos injected with short dsRNA showed a characteristic phenotype of enlarged anterior structures and loss of posterior structures. These phenotypes, as well as the increased expression of the anterior gene and decreased expression of the posterior gene, suggest that RNAi against the β-catenin gene suppresses the "late Wnt signaling" involved in proper anterior-posterior patterning of Xenopus embryos. The effect of RNAi on Xenopus embryos was also found to be sensitive to temperature. These results strongly suggest that the RNAi technique can be applied to Xenopus embryos using short dsRNAs, appropriate temperature control, and proper selection of target genes.

Long Non-Coding RNAs in Cardiovascular Diseases: Potential Function as Biomarkers and Therapeutic Targets of Exercise Training

Despite advances in treatments and therapies, cardiovascular diseases (CVDs) remain one of the leading causes of death worldwide. The discovery that most of the human genome, although transcribed, does not encode proteins was crucial for focusing on the potential of long non-coding RNAs (lncRNAs) as essential regulators of cell function at the epigenetic, transcriptional, and post-transcriptional levels. This class of non-coding RNAs is related to the pathophysiology of the cardiovascular system. The different expression profiles of lncRNAs, in different contexts of CVDs, change a great potential in their use as a biomarker and targets of therapeutic intervention. Furthermore, regular physical exercise plays a protective role against CVDs; on the other hand, little is known about its underlying molecular mechanisms. In this review, we look at the accumulated knowledge on lncRNAs and their functions in the cardiovascular system, focusing on the cardiovascular pathology of arterial hypertension, coronary heart disease, acute myocardial infarction, and heart failure. We discuss the potential of these molecules as biomarkers for clinical use, their limitations, and how the manipulation of the expression profile of these transcripts through physical exercise can begin to be suggested as a strategy for the treatment of CVDs.

Debugging: Strategies and Considerations for Efficient RNAi-Mediated Control of the Whitefly Bemisia tabaci

The whitefly Bemisia tabaci is a globally important pest that is difficult to control through insecticides, transgenic crops, and natural enemies. Post-transcriptional gene silencing through RNA interference (RNAi) has shown potential as a pest management strategy against B. tabaci. While genomic data and other resources are available to create highly effective customizable pest management strategies with RNAi, current applications do not capitalize on species-specific biology. This lack of specificity has the potential to have substantial ecological impacts. Here, we discuss both short- and long-term considerations for sustainable RNAi pest management strategies for B. tabaci, focusing on the need for species specificity incorporating both life history and population genetic considerations. We provide a conceptual framework for selecting sublethal target genes based on their involvement in physiological pathways, which has the greatest potential to ameliorate unintended negative consequences. We suggest that these considerations allow an integrated pest management approach, with fewer negative ecological impacts and reduced likelihood of the evolution of resistant populations.

Nanocarriers in effective pulmonary delivery of siRNA: current approaches and challenges

Research on siRNA is increasing due to its wide applicability as a therapeutic agent in irreversible medical conditions. siRNA inhibits expression of the specific gene after its delivery from formulation to cytosol region of a cell. RNAi (RNA interference) is a mechanism by which siRNA is silencing gene expression for a particular disease. Numerous studies revealed that naked siRNA delivery is not preferred due to instability and poor pharmacokinetic performance. Nanocarriers based delivery of siRNA has the advantage to overcome physiological barriers and protect the integrity of siRNA from degradation by RNAase. Various diseases like lung cancer, cystic fibrosis, asthma, etc can be treated effectively by local lung delivery. The selective targeted therapeutic action in diseased organ and least off targeted cytotoxicity are the key benefits of pulmonary delivery. The current review highlights recent developments in pulmonary delivery of siRNA with novel nanosized formulation approach with the proven in vitro/in vivo applications.

Characterising the effect of Akirin knockdown on Anopheles arabiensis (Diptera: Culicidae) reproduction and survival, using RNA-mediated interference

Anopheles arabiensis is an opportunistic malaria vector that rests and feeds outdoors, circumventing current vector control methods. Furthermore, this vector will readily feed on animal as well as human hosts. Targeting the vector, while feeding on animals, can provide an additional intervention for the current vector control activities. Agricultural animals are regularly vaccinated with recombinant proteins for the control of multiple endo- and ecto-parasitic infestations. The use of a Subolesin-vaccine showed a mark reduction in tick reproductive fitness. The orthologous gene of Subolesin, called Akirin in insects, might provide a valuable species-specific intervention against outdoor biting An. arabiensis. However, the biological function of this nuclear protein has not yet been investigated in this mosquito. The effects on An. arabiensis lifetable parameters were evaluated after Akirin was knocked down using commercial small-interfering RNA (siRNA) and in vitro transcribed double-stranded RNA (dsRNA). The siRNA mediated interference of Akirin significantly reduced fecundity by 17%, fertility by 23% and longevity by 32% when compared to the controls in the female mosquitoes tested. Similarly, dsRNA treatment had a 25% decrease in fecundity, 29% decrease in fertility, and 48% decrease in longevity, when compared to the control treatments. Mosquitoes treated with Akirin dsRNA had a mean survival time of 15-days post-inoculation, which would impact on their ability to transmit malaria parasites. These results strongly suggest that Akirin has a pleiotropic function in An. arabiensis longevity and reproductive fitness.

Virus-induced gene silencing (VIGS) in Cannabis sativa L

BACKGROUND

The raised demand of cannabis as a medicinal plant in recent years led to an increased interest in understanding the biosynthetic routes of cannabis metabolites. Since there is no established protocol to generate stable gene knockouts in cannabis, the use of a virus-induced gene silencing (VIGS) method, resulting in a gene knockdown, to study gene functions is desirable.

RESULTS

For this, a computational approach was employed to analyze the Cannabis sativa L. transcriptomic and genomic resources. Reporter genes expected to give rise to easily scorable phenotypes upon silencing, i.e. the phytoene desaturase (PDS) and magnesium chelatase subunit I (ChlI), were identified in C. sativa. Subsequently, the targets of specific small interfering RNAs (siRNAs) and silencing fragments were predicted and tested in a post-transcriptional gene silencing (PTGS) approach. Here we show for the first time a gene knockdown in C. sativa using the Cotton leaf crumple virus (CLCrV) in a silencing vector system. Plants transiently transformed with the Agrobacterium tumefaciens strain AGL1, carrying the VIGS-vectors, showed the desired phenotypes, spotted bleaching of the leaves. The successful knockdown of the genes was additionally validated by quantitative PCR resulting in reduced expression of transcripts from 70 to 73% for ChlI and PDS, respectively. This is accompanied with the reduction of the chlorophyll a and carotenoid content, respectively. In summary, the data clearly demonstrate the potential for functional gene studies in cannabis using the CLCrV-based vector system.

CONCLUSIONS

The applied VIGS-method can be used for reverse genetic studies in C. sativa to identify unknown gene functions. This will gain deeper inside into unknown biosynthetic routes and will help to close the gap between available genomic data and biochemical information of this important medicinal plant.

Genome-wide identification and analysis of genes associated with RNA interference in Bemisia tabaci

BACKGROUND

As a method of RNA-mediated gene silencing, RNA interference (RNAi) is a useful reverse genetic tool with which to study gene function, and holds great promise for pest management. Bemisia tabaci is a cosmopolitan pest that causes extensive damage to crops. The mechanism underlying RNAi efficiency in B. tabaci is not well known. We identified and analyzed candidate genes in the RNAi pathway to understand the RNAi mechanism and provide a basis for the application of RNAi in pest management.

RESULTS

We identified 33 genes putatively involved in the RNAi pathway from the B. tabaci Q genome. Phylogenetic and structural analyses confirmed the characteristics of these genes. Furthermore, quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) and transcriptomic analysis profiled gene expression patterns during different developmental stages. Gene expression levels estimated by qRT-PCR and RNA-seq analyses were significantly correlated. Moreover, gene functions were verified by RNAi. When accompanied by knockdown of AGO2, Dicer2 and Sid1, the efficiency of CYP6DB3 RNAi decreased correspondingly.

CONCLUSION

In this study, we annotated and validated genes involved in B. tabaci RNAi. A better understanding of the building blocks of the RNAi process in B. tabaci facilitates integration of this novel biotechnology into the management of this emerging pest, either directly or indirectly. © 2019 Society of Chemical Industry.

Invasive Insects: Management Methods Explored

Invasive insect species can act as a plague across the globe, capable of vast expansion and rapid, proliferate reproduction. The spread of pathogens of serious diseases such as malaria and Zika virus and damages to agricultural crops number some of the afflictions invasive insects provide to humans alone. Additionally, an escape from predators can fail to keep invasive insects in check, providing potential threats such as extra resource competition to native species when insects invade. A variety of methods are employed to combat these invasive species, each with their own varying levels of success. Here, we explore the more traditional methods of invasive insect pest control, such as pesticides and biological control. In lieu of several unintended consequences resulting from such practices, we suggest some should be abandoned. We evaluate the potential of new techniques, in particular, those with a genetic component, regarding the costs, benefits and possible consequences of implementing them. And finally, we consider which techniques should be the focus of future research, if we truly wish to manage or even eradicate invasive insects in their introduced lands.

Delivery of a Genetically Marked Serratia AS1 to Medically Important Arthropods for Use in RNAi and Paratransgenic Control Strategies

Understanding how arthropod vectors acquire their bacteria is essential for implementation of paratransgenic and RNAi strategies using genetically modified bacteria to control vector-borne diseases. In this study, a genetically marked Serratia AS1 strain expressing the mCherry fluorescent protein (mCherry-Serratia) was used to test various acquisition routes in six arthropod vectors including Anopheles stephensi, Culex pipiens, Cx. quinquefaciatus, Cx. theileri, Phlebotomus papatasi, and Hyalomma dromedarii. Depending on the species, the bacteria were delivered to (i) mosquito larval breeding water, (ii) host skin, (iii) sugar bait, and (iv) males (paratransgenic). The arthropods were screened for the bacteria in their guts or other tissues. All the hematophagous arthropods were able to take the bacteria from the skin of their hosts while taking blood meal. The mosquitoes were able to take up the bacteria from the water at larval stages and to transfer them transstadially to adults and finally to transfer them to the water they laid eggs in. The mosquitoes were also able to acquire the bacteria from male sperm. The level of bacterial acquisition was influenced by blood feeding time and strategies (pool or vessel feeding), dipping in water and resting time of newly emerged adult mosquitoes, and the disseminated tissue/organ. Transstadial, vertical, and venereal bacterial acquisition would increase the sustainability of the modified bacteria in vector populations and decrease the need for supplementary release experiments whereas release of paratransgenic males that do not bite has fewer ethical issues. Furthermore, this study is required to determine if the modified bacteria can be introduced to arthropods in the same routes in nature.

Effect of Serratia AS1 (Enterobacteriaceae: Enterobacteriales) on the Fitness of Culex pipiens (Diptera: Culicidae) for Paratransgenic and RNAi Approaches

The mosquito Culex pipiens is the primary vector of Rift Valley fever, West Nile, encephalitis, and Zika viruses, and periodic lymphatic filariasis. Developing insecticide resistance in mosquitoes demands the development of new approaches to fight these diseases. Paratransgenesis and RNAi approaches by using engineered bacteria have been shown to reduce mosquito vector competence. Serratia-AS1 is a bacterium found in mosquitoes and was genetically modified for expression of antimalaria effector molecules that repress development of malaria parasites in mosquitoes. The aim of this study was to determine how a genetically marked Serratia strain expressing the mCherry fluorescent protein (mCherry-Serratia) affects the colonization potential, life span, blood feeding behavior, fecundity, and fertility of Cx. pipiens. mCherry-Serratia bacteria disseminated into larvae, pupae, and newly emerged adults and dramatically increased in numbers following a blood meal. The bacterium was transmitted to progeny, showing that it can extend horizontally, transstadially, and vertically through the mosquito population. The presence of mCherry-Serratia did not affect blood feeding behavior, survival rate, fecundity, and fertility of Culex mosquitoes. This is the first study to evaluate the effects of an engineered bacteria on the fitness of Cx. pipiens. Although challenges remain, such as producing engineered bacteria to secrete anti-pathogens associated with Cx. pipiens, introducing such bacteria into mosquito populations, our findings of minimal fitness cost caused by Serratia-AS1 bode well for the development of paratransgenesis and RNAi approaches.

RNA interference of endoglucanases in the formosan subterranean termite Coptotermes formosanus shiraki (Blattodea: Rhinotermitidae) by dsRNA injection or ingestion

Termites obtain energy and nutrition from wood and wood-related materials by utilizing endogenous and symbiotic cellulases. Endoglucanase is one of the key cellulases in cellulose digestion. Previous studies have shown that the inhibition of the cellulase enzyme system would be a plausible approach for termite control. In the present study, we studied the effect of RNAi on termites by targeting a conserved region of five endoglucanase genes from Coptotermes formosanus (CfEGs). Both dsRNA injection and oral delivery resulted in significant gene silencing of CfEGs and consequently led to mortality, reduced enzyme activity, and reduced weight compared to control worker termites. An injection dose of 150 ng and a feeding dose of 2 μg/cm² provided for the best RNAi efficiency. dsCfEG was further combined with flufenoxuron, an insect growth regulator used to manage/suppress subterranean termites, and when fed to workers, caused a lower enzyme activity compared to the dsCfEG- or flufenoxuron-only treatment. The weight loss (∼0.598 mg) and mortality (∼28%) observed in the combined dsCfEG and flufenoxuron treatment differed significantly from those observed in the flufenoxuron-only treatment (∼0.208 mg and ∼16%, respectively). Although the effects of these dsCfEG treatments on mortality were insufficient to serve as termiticides, dsCfEGs could be used in combination with other treatments to increase efficacy. This study provides a research basis for the use of RNAi in termiticides.

Long Noncoding RNAs and Cardiac Disease

SIGNIFICANCE

To maintain homeostasis, gene expression has to be tightly regulated by complex and multiple mechanisms occurring at the epigenetic, transcriptional, and post-transcriptional levels. One crucial regulatory component is represented by long noncoding RNAs (lncRNAs), nonprotein-coding RNA species implicated in all of these levels. Thus, lncRNAs have been associated with any given process or pathway of interest in a variety of systems, including the heart. Recent Advances: Mounting evidence implicates lncRNAs in cardiovascular diseases (CVD) and progression and their presence in the blood of heart disease patients indicates that they are attractive potential biomarkers.

CRITICAL ISSUES

Our understanding of the regulation and molecular mechanisms of action of most lncRNAs remains rudimentary. A challenge is represented by their often low evolutionary sequence conservation that limits the use of animal models for preclinical studies. Nevertheless, a growing number of lncRNAs with an impact on heart function is rapidly accumulating. In this study, we will discuss (i) lncRNAs that control heart homeostasis and disease; (ii) concepts, approaches, and methodologies necessary to study lncRNAs in the heart; and (iii) challenges posed and opportunities presented by lncRNAs as potential therapeutic targets and biomarkers.

FUTURE DIRECTIONS

A deeper knowledge of the molecular mechanisms underpinning CVDs is necessary to develop more effective treatments. Further studies are needed to clarify the regulation and function of lncRNAs in the heart before they can be considered as therapeutic targets and disease biomarkers. Antioxid. Redox Signal. 29, 880-901.

Reverse genetics demonstrate the role of mucosal C-type lectins in food particle selection in the oyster Crassostrea virginica

Prey selection governs species interactions and regulates physiological energetics of individuals and populations. Suspension-feeding bivalves represent key species in coastal and estuarine systems for their ecological and economic value. These animals are able to sort and selectively ingest nutritious microalgae from dilute and composite mixtures of particulate matter. This aptitude was suggested to be mediated by interactions between carbohydrates associated with the surface of microalgae and C-type lectins present in mucus covering the feeding organs although a direct, unequivocal, role of lectins in food sorting in bivalves remains elusive. This study was designed to identify and characterize mucosal C-type lectins from oysters and manipulate the expression of these proteins in order to obtain decisive information regarding their involvement in food choice. Thus, 2 mucosal C-type lectins (CvML3912 and CvML3914) were identified based on transcriptomic and proteomic information. Transcripts of these lectins were detected in the feeding organs and their expression was upregulated following starvation. Recombinant lectin (rCvML3912) competitively inhibited the binding of commercial mannose/glucose-specific lectins to microalgae. Short DsiRNA targeting these two lectins were designed and used to evaluate the effect of gene silencing on food particle sorting. As a result, the abundance of the two cognate transcripts significantly decreased and food sorting ability was significantly reduced among silenced oysters as compared to control animals. Overall, these findings propose a novel concept establishing the role of carbohydrate-protein interactions to provide an efficient food particle sorting, and establish a new dimension for the role of evolutionarily-conserved mannose/glucose-binding proteins in the metazoan.

Insect RNAi: Integrating a New Tool in the Crop Protection Toolkit

Protecting crops against insect pests is a major focus area in crop protection. Over the past two decades, biotechnological interventions, especially Bt proteins, have been successfully implemented across the world and have had major impacts on reducing chemical pesticide applications. As insects continue to adapt to insecticides, both chemical and protein-based, new methods, molecules, and modes of action are necessary to provide sustainable solutions. RNA interference (RNAi) has emerged as a significant tool to knock down or alter gene expression profiles in a species-specific manner. In the past decade, there has been intense research on RNAi applications in crop protection. This chapter looks at the current state of knowledge in the field and outlines the methodology, delivery methods, and precautions required in designing targets. Assessing the targeting of specific gene expression is also an important part of a successful RNAi strategy. The current literature on the use of RNAi in major orders of insect pests is reviewed, along with a perspective on the regulatory aspects of the approach. Risk assessment of RNAi would focus on molecular characterization, food/feed risk assessment, and environmental risk assessment. As more RNAi-based products come through regulatory systems, either via direct application or plant expression based, the impact of this approach on crop protection will become clearer.

5΄-Vinylphosphonate improves tissue accumulation and efficacy of conjugated siRNAs in vivo

5΄-Vinylphosphonate modification of siRNAs protects them from phosphatases, and improves silencing activity. Here, we show that 5΄-vinylphosphonate confers novel properties to siRNAs. Specifically, 5΄-vinylphosphonate (i) increases siRNA accumulation in tissues, (ii) extends duration of silencing in multiple organs and (iii) protects siRNAs from 5΄-to-3΄ exonucleases. Delivery of conjugated siRNAs requires extensive chemical modifications to achieve stability in vivo. Because chemically modified siRNAs are poor substrates for phosphorylation by kinases, and 5΄-phosphate is required for loading into RNA-induced silencing complex, the synthetic addition of a 5΄-phosphate on a fully modified siRNA guide strand is expected to be beneficial. Here, we show that synthetic phosphorylation of fully modified cholesterol-conjugated siRNAs increases their potency and efficacy in vitro, but when delivered systemically to mice, the 5΄-phosphate is removed within 2 hours. The 5΄-phosphate mimic 5΄-(E)-vinylphosphonate stabilizes the 5΄ end of the guide strand by protecting it from phosphatases and 5΄-to-3΄ exonucleases. The improved stability increases guide strand accumulation and retention in tissues, which significantly enhances the efficacy of cholesterol-conjugated siRNAs and the duration of silencing in vivo. Moreover, we show that 5΄-(E)-vinylphosphonate stabilizes 5΄ phosphate, thereby enabling systemic delivery to and silencing in kidney and heart.

Trends in the Binding of Cell Penetrating Peptides to siRNA: A Molecular Docking Study

The use of gene therapeutics, including short interfering RNA (siRNA), is limited by the lack of efficient delivery systems. An appealing approach to deliver gene therapeutics involves noncovalent complexation with cell penetrating peptides (CPPs) which are able to penetrate the cell membranes of mammals. Although a number of CPPs have been discovered, our understanding of their complexation and translocation of siRNA is as yet insufficient. Here, we report on computational studies comparing the binding affinities of CPPs with siRNA, considering a variety of CPPs. Specifically, seventeen CPPs from three different categories, cationic, amphipathic, and hydrophobic CPPs, were studied. Molecular mechanics were used to minimize structures, while molecular docking calculations were used to predict the orientation and favorability of sequentially binding multiple peptides to siRNA. Binding scores from docking calculations were highest for amphipathic peptides over cationic and hydrophobic peptides. Results indicate that initial complexation of peptides will likely occur along the major groove of the siRNA, driven by electrostatic interactions. Subsequent binding of CPPs is likely to occur in the minor groove and later on bind randomly, to siRNA or previously bound CPPs, through hydrophobic interactions. However, hydrophobic CPPs do not show this binding pattern. Ultimately binding yields a positively charged nanoparticle capable of noninvasive cellular import of therapeutic molecules.

RNA interference influenced the proliferation and invasion of XWLC-05 lung cancer cells through inhibiting aquaporin 3

OBJECTIVE

The objective of this study was to construct a recombinant vector expressing siRNA targetedly inhibiting aquaporin 3 (AQP3), and to evaluate the effects of AQP3 inhibition on the proliferation and invasion of XWLC-05 human lung cancer cells.

METHODS

We obtained human AQP3 sequence from the Genbank and established the recombinant vector expressing siRNA targeting AQP3. After the transfection of the recombinant vectors, the expression of AQP3 was determined by RT-PCR and western blot. The MTS assay, flow cytometry and Transwell assay were conducted to detect the proliferation, cell cycle process, apoptosis and invasion of XWLC-05 cells. Then the activity of metal matrix proteinase (MMP) 2 was determined by gelatin zymography. Tumor formation in vivo experiments were also conducted in nude mice.

RESULTS

RNA interference (RNAi) of AQP3 substantially suppressed the XWLC-05 cell proliferation and invasion, blocked the cell cycle progressing and promoted cell apoptosis. In addition, the activity of MMP2 was remarkably attenuated in RNAi group. AQP3 RNAi did not affect the tumor formation rate in nude mice but reduced the tumor growth.

CONCLUSION

The inhibition of AQP3 retarded the growth and invasiveness of XWLC-05 lung cancer cells and decreased the activity of MMP2.

Effects of RNA silencing of matrix metalloproteinase-2 on the growth of esophageal carcinoma cells in vivo

Esophageal carcinoma is one of the most common malignancies in China. Previous studies reported that matrix metalloproteinases (MMPs) have important roles in the progression and invasion of numerous types of solid tumors. Among the MMPs, MMP-2 has been closely associated with tumor growth and invasion. In the present study, a short hairpin RNA (shRNA) lentiviral expression vector targeting the MMP-2 gene was constructed in order to observe the inhibitory effect of MMP-2 gene silencing on the growth of the KYSE150 esophageal carcinoma cell line in vivo. Three small hairpin RNA sequences targeting MMP-2 were designed and cloned into lentiviral vectors. Following transfection of the lentiviral vectors into KTSE150 cells, MMP-2 mRNA and protein expression levels were examined by reverse transcription-quantitative polymerase chain reaction and western blotting, and the growth rate of cells was analyzed by MTT assays. Subsequently, tumor growth was assessed in nude mice. Lentivirus-mediated RNA interference effectively inhibited the expression of MMP-2 mRNA and protein in KYSE150 esophageal carcinoma cells, and suppressed the growth of esophageal carcinoma cells in vivo. The results of the present study suggested that lentivirus-mediated gene therapy targeting MMP-2 may be an attractive strategy for the treatment of esophageal carcinoma and justifies the performance of further studies on the application of lentivirus vectors to cancer gene therapy.

shRNA mediated knockdown of Nav1.7 in rat dorsal root ganglion attenuates pain following burn injury

Background

Abnormal acute pain after burn injury still torments patients severely. In this study, we investigated that one voltage gated sodium channel Nav1.7 plays a vital role in lowering heat pain threshold after burn injury, and the hypothesis that knockdown of Nav1.7 attenuates pain following burn injury.

Methods

Sixty eight adult male Sprague–Dawley rats were divided into 4 treatment groups: (1) sham, which hind paw was put on the room temperature metal plate for 15 s (2) burn model, which hind paw was put on the 85 °C metal plate for 15 s. (3) Burn injury + lentiviral vector -SCN9AsiRNA-GFP (LV- SCN9AsiRNA-GFP group, n = 18), which receive the DRG microinjection of LV- SCN9AsiRNA-GFP on the zero day. (4) Burn injury + lentiviral vector negative control (LV-NC-GFP group, n = 18), which receive the DRG microinjection of empty lentiviral vector on the zero day.

Results

Both mechanical and heat threshold were measured from day 1 to 21. Meanwhile, expression of sodium channels Nav1.7 in injured dorsal root ganglia were measured on post-operative days 7(POD 7). Rats exhibited decreased thresholds on both mechanical allodynia and thermal withdrawl latency, accompanied by increased Nav1.7 and c-fos expression in dorsal root ganglion (DRG). And knockdown of Nav1.7 in L5DRG led to the attenuation of burn injury-induced mechanical allodynia and thermal hyperalgesia in the rats.

Conclusion

We provide evidence that shRNA mediated knockdown of Nav1.7 attenuates burn induced pain in rats as well as decreased the activiation of c-fos protein.

AAV9 Delivery of shRNA to the Mouse Heart

RNA interference (RNAi) is a rapid approach to dissect loss-of-function phenotype for a gene of interest. However, it is challenging to perform RNAi in specific organs and tissues in vivo. Engineered viruses can provide a useful tool for delivery of small RNAs in vivo. Recombinant adeno-associated viruses (rAAVs) are the preferred method for delivering genes or gene modulators to target cells due to their high titer, low immune response, ability to transduce many types of cell, and overall safety. In this unit, we describe protocols for use of rAAVs as a cargo to deliver miRNA backbone-based shRNA controlled by a cardiac-specific promoter into the mouse heart. © 2016 by John Wiley & Sons, Inc.

Reduced stability and intracellular transport of dsRNA contribute to poor RNAi response in lepidopteran insects

RNA interference (RNAi) has become a widely used reverse genetic tool to study gene function in eukaryotic organisms and is being developed as a technology for insect pest management. The efficiency of RNAi varies among organisms. Insects from different orders also display differential efficiency of RNAi, ranging from highly efficient (coleopterans) to very low efficient (lepidopterans). We investigated the reasons for varying RNAi efficiency between lepidopteran and coleopteran cell lines and also between the Colorado potato beetle, Leptinotarsa decemlineata and tobacco budworm, Heliothis virescens. The dsRNA either injected or fed was degraded faster in H. virescens than in L. decemlineata. Both lepidopteran and coleopteran cell lines and tissues efficiently took up the dsRNA. Interestingly, the dsRNA administered to coleopteran cell lines and tissues was taken up and processed to siRNA whereas the dsRNA was taken up by lepidopteran cell lines and tissues but no siRNA was detected in the total RNA isolated from these cell lines and tissues. The data included in this paper showed that the degradation and intracellular transport of dsRNA are the major factors responsible for reduced RNAi efficiency in lepidopteran insects.

Molecular genetic models related to schizophrenia and psychotic illness: heuristics and challenges

Schizophrenia is a heritable disorder that may involve several common genes of small effect and/or rare copy number variation, with phenotypic heterogeneity across patients. Furthermore, any boundaries vis-à-vis other psychotic disorders are far from clear. Consequently, identification of informative animal models for this disorder, which typically relate to pharmacological and putative pathophysiological processes of uncertain validity, faces considerable challenges. In juxtaposition, the majority of mutant models for schizophrenia relate to the functional roles of a diverse set of genes associated with risk for the disorder or with such putative pathophysiological processes. This chapter seeks to outline the evidence from phenotypic studies in mutant models related to schizophrenia. These have commonly assessed the degree to which mutation of a schizophrenia-related gene is associated with the expression of several aspects of the schizophrenia phenotype or more circumscribed, schizophrenia-related endophenotypes; typically, they place specific emphasis on positive and negative symptoms and cognitive deficits, and extend to structural and other pathological features. We first consider the primary technological approaches to the generation of such mutants, to include their relative merits and demerits, and then highlight the diverse phenotypic approaches that have been developed for their assessment. The chapter then considers the application of mutant phenotypes to study pathobiological and pharmacological mechanisms thought to be relevant for schizophrenia, particularly in terms of dopaminergic and glutamatergic dysfunction, and to an increasing range of candidate susceptibility genes and copy number variants. Finally, we discuss several pertinent issues and challenges within the field which relate to both phenotypic evaluation and a growing appreciation of the functional genomics of schizophrenia and the involvement of gene × environment interactions.

Hydrophobically Modified siRNAs Silence Huntingtin mRNA in Primary Neurons and Mouse Brain

Applications of RNA interference for neuroscience research have been limited by a lack of simple and efficient methods to deliver oligonucleotides to primary neurons in culture and to the brain. Here, we show that primary neurons rapidly internalize hydrophobically modified siRNAs (hsiRNAs) added directly to the culture medium without lipid formulation. We identify functional hsiRNAs targeting the mRNA of huntingtin, the mutation of which is responsible for Huntington's disease, and show that direct uptake in neurons induces potent and specific silencing in vitro. Moreover, a single injection of unformulated hsiRNA into mouse brain silences Htt mRNA with minimal neuronal toxicity. Thus, hsiRNAs embody a class of therapeutic oligonucleotides that enable simple and straightforward functional studies of genes involved in neuronal biology and neurodegenerative disorders in a native biological context.

An Efficient Method for Electroporation of Small Interfering RNAs into ENCODE Project Tier 1 GM12878 and K562 Cell Lines

The Encyclopedia of DNA Elements (ENCODE) Project aims to identify all functional sequence elements in the human genome sequence by use of high-throughput DNA/cDNA sequencing approaches. To aid the standardization, comparison, and integration of data sets produced from different technologies and platforms, the ENCODE Consortium selected several standard human cell lines to be used by the ENCODE Projects. The Tier 1 ENCODE cell lines include GM12878, K562, and H1 human embryonic stem cell lines. GM12878 is a lymphoblastoid cell line, transformed with the Epstein-Barr virus, that was selected by the International HapMap Project for whole genome and transcriptome sequencing by use of the Illumina platform. K562 is an immortalized myelogenous leukemia cell line. The GM12878 cell line is attractive for the ENCODE Projects, as it offers potential synergy with the International HapMap Project. Despite the vast amount of sequencing data available on the GM12878 cell line through the ENCODE Project, including transcriptome, chromatin immunoprecipitation-sequencing for histone marks, and transcription factors, no small interfering siRNA-mediated knockdown studies have been performed in the GM12878 cell line, as cationic lipid-mediated transfection methods are inefficient for lymphoid cell lines. Here, we present an efficient and reproducible method for transfection of a variety of siRNAs into the GM12878 and K562 cell lines, which subsequently results in targeted protein depletion.

Gene silencing by RNA interference in the house dust mite, Dermatophagoides pteronyssinus

This is the first report of gene silencing by RNA interference (RNAi) in the European house dust mite, Dermatophagoides pteronyssinus, Trouessart, 1897. Using a non-invasive immersion method first developed for the honey bee mite, Varroa destructor, a significant reduction in the expression of D. pteronyssinus glutathione-S-transferase mu-class 1 enzyme (DpGST-mu1) was achieved following overnight immersion in double stranded RNA encoding DpGST-mu1. Although no detrimental phenotypic changes were observed following silencing, this technique can now be used to address fundamental physiological questions and assess the potential therapeutic benefit in silencing D. pteronyssinus target genes in selected domestic situations of high human-mite interface.

A critical domain of Sweet potato chlorotic fleck virus nucleotide-binding protein (NaBp) for RNA silencing suppression, nuclear localization and viral pathogenesis

RNA silencing is an important mechanism of antiviral defence in plants. To counteract this resistance mechanism, many viruses have evolved RNA silencing suppressors. In this study, we analysed five proteins encoded by Sweet potato chlorotic fleck virus (SPCFV) for their abilities to suppress RNA silencing using a green fluorescent protein (GFP)-based transient expression assay in Nicotiana benthamiana line 16c plants. Our results showed that a putative nucleotide-binding protein (NaBp), but not other proteins encoded by the virus, could efficiently suppress local and systemic RNA silencing induced by either sense or double-stranded RNA (dsRNA) molecules. Deletion mutation analysis of NaBp demonstrated that the basic motif (an arginine-rich region) was critical for its RNA silencing suppression activity. Using confocal laser scanning microscopy imaging of transfected protoplasts expressing NaBp fused to GFP, we showed that NaBp accumulated predominantly in the nucleus. Mutational analysis of NaBp demonstrated that the basic motif represented part of the nuclear localization signal. In addition, we demonstrated that the basic motif in NaBp was a pathogenicity determinant in the Potato virus X (PVX) heterogeneous system. Overall, our results demonstrate that the basic motif of SPCFV NaBp plays a critical role in RNA silencing suppression, nuclear localization and viral pathogenesis.

Satellite RNAs interfere with the function of viral RNA silencing suppressors

Viral satellite RNAs (satRNAs) are small subviral RNAs and depend on the helper virus for replication and spread. satRNAs can attenuate helper virus-induced symptoms, the mechanism of which remains unclear. Here, we show that two virus-encoded suppressors of RNA silencing (VSRs), Cucumber mosaic virus (CMV) 2b and Tombusvirus P19, suppress hairpin RNA (hpRNA)-induced silencing of a β-glucuronidase (GUS) gene in Nicotiana benthamiana. This suppression can be overcome by CMV Y-satellite RNA (Y-Sat) via the Y-Sat-derived small interfering RNAs (siRNAs), which bind to the VSRs and displace the bound hpGUS-derived siRNAs. We also show that microRNA target gene expression in N. tabacum was elevated by CMV infection, presumably due to function of the 2b VSR, but this upregulation of microRNA target genes was reversed in the presence of Y-Sat. These results suggest that satRNA infection minimizes the effect of VSRs on host siRNA and microRNA-directed silencing. Our results suggest that the high abundance of satRNA-derived siRNAs contributes to symptom attenuation by binding helper virus-encoded VSRs, minimizing the capacity of the VSRs to bind host siRNA and miRNA and interfere with their function.

RNA interference for the identification of ectoparasite vaccine candidates

Ectoparasites present a major challenge for disease management globally. With drug resistance increasingly observed in many disease-causing species, the need for novel control measures is pressing. Ever-expanding genomic resources from 'next generation' sequencing are now available for a number of arthropod ectoparasites, necessitating an effective means of screening these data for novel candidates for vaccine antigens or targets for chemotherapeutics. Such in vitro screening methods must be developed if we are to make discoveries in a timely and cost-effective manner. This review will discuss the potential that RNA interference (RNAi) has demonstrated thus far in the context of arthropod ectoparasites and the potential roles for this technology in the development of novel methods for parasite control.

Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice

BACKGROUND

Endogenous small (sm) RNAs (primarily si- and miRNAs) are important trans/cis-acting regulators involved in diverse cellular functions. In plants, the RNA-dependent RNA polymerases (RDRs) are essential for smRNA biogenesis. It has been established that RDR2 is involved in the 24 nt siRNA-dependent RNA-directed DNA methylation (RdDM) pathway. Recent studies have suggested that RDR1 is involved in a second RdDM pathway that relies mostly on 21 nt smRNAs and functions to silence a subset of genomic loci that are usually refractory to the normal RdDM pathway in Arabidopsis. Whether and to what extent the homologs of RDR1 may have similar functions in other plants remained unknown.

RESULTS

We characterized a loss-of-function mutant (Osrdr1) of the OsRDR1 gene in rice (Oryza sativa L.) derived from a retrotransposon Tos17 insertion. Microarray analysis identified 1,175 differentially expressed genes (5.2% of all expressed genes in the shoot-tip tissue of rice) between Osrdr1 and WT, of which 896 and 279 genes were up- and down-regulated, respectively, in Osrdr1. smRNA sequencing revealed regional alterations in smRNA clusters across the rice genome. Some of the regions with altered smRNA clusters were associated with changes in DNA methylation. In addition, altered expression of several miRNAs was detected in Osrdr1, and at least some of which were associated with altered expression of predicted miRNA target genes. Despite these changes, no phenotypic difference was identified in Osrdr1 relative to WT under normal condition; however, ephemeral phenotypic fluctuations occurred under some abiotic stress conditions.

CONCLUSIONS

Our results showed that OsRDR1 plays a role in regulating a substantial number of endogenous genes with diverse functions in rice through smRNA-mediated pathways involving DNA methylation, and which participates in abiotic stress response.

A co-CRISPR strategy for efficient genome editing in Caenorhabditis elegans

Genome editing based on CRISPR (clustered regularly interspaced short palindromic repeats)-associated nuclease (Cas9) has been successfully applied in dozens of diverse plant and animal species, including the nematode Caenorhabditis elegans. The rapid life cycle and easy access to the ovary by micro-injection make C. elegans an ideal organism both for applying CRISPR-Cas9 genome editing technology and for optimizing genome-editing protocols. Here we report efficient and straightforward CRISPR-Cas9 genome-editing methods for C. elegans, including a Co-CRISPR strategy that facilitates detection of genome-editing events. We describe methods for detecting homologous recombination (HR) events, including direct screening methods as well as new selection/counterselection strategies. Our findings reveal a surprisingly high frequency of HR-mediated gene conversion, making it possible to rapidly and precisely edit the C. elegans genome both with and without the use of co-inserted marker genes.

Mla- and Rom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus

• Barley (Hordeum vulgare L.) Mildew resistance locus a (Mla) confers allele-specific interactions with natural variants of the ascomycete fungus Blumeria graminis f. sp. hordei (Bgh), the causal agent of powdery mildew disease. Significant reprogramming of Mla-mediated gene expression occurs upon infection by this obligate biotrophic pathogen. • We utilized a proteomics-based approach, combined with barley mla, required for Mla12 resistance1 (rar1), and restoration of Mla resistance1 (rom1) mutants, to identify components of Mla-directed signaling. • Loss-of-function mutations in Mla and Rar1 both resulted in the reduced accumulation of chloroplast copper/zinc superoxide dismutase 1 (HvSOD1), whereas loss of function in Rom1 re-established HvSOD1 levels. In addition, both Mla and Rom1 negatively regulated hvu-microRNA398 (hvu-miR398), and up-regulation of miR398 was coupled to reduced HvSOD1 expression. Barley stripe mosaic virus (BSMV)-mediated over-expression of both barley and Arabidopsis miR398 repressed accumulation of HvSOD1, and BSMV-induced gene silencing of HvSod1 impeded Mla-triggered H₂O₂ and hypersensitive reaction (HR) at barley-Bgh interaction sites. • These data indicate that Mla- and Rom1-regulated hvu-miR398 represses HvSOD1 accumulation, influencing effector-induced HR in response to the powdery mildew fungus.

Development of a microinjection system for RNA interference in the water flea Daphnia pulex

Background

The ubiquitous, freshwater microcrustacean Daphnia pulex provides a model system for both human health research and monitoring ecosystem integrity. It is the first crustacean to have a well annotated, reference genome assembly that revealed an unusually high gene count highlighted by a large gene orphanage,-i.e., previously uncharacterized genes. Daphnia are capable of either clonal or sexual reproduction, making them ideally suited for genetic manipulation, but the establishment of gene manipulation techniques is needed to accurately define gene functions. Although previous investigations developed an RNA interference (RNAi) system for one congener D. magna, these methods are not appropriate for D. pulex because of the smaller size of their early embryos. In these studies, we develop RNAi techniques for D. pulex by first determining the optimum culture conditions of their isolated embryos and then applying these conditions to the development of microinjection techniques and proof-of-principle RNAi experiments.

Results

We found that isolated embryos were best cultured on a 2% agar plate bathed in 60 mM sucrose dissolved in M4 media, providing optimal conditions for microinjections. Then, we injected double-stranded (ds)RNA specific to the Distal-less gene (Dll), which is a homeobox transcription factor essential for limb development in invertebrates and vertebrates. Injected embryos presented with defects in the second antenna and appendage development, and dsRNA induced the degradation of Dll mRNAs, indicating that this technique successfully inhibited transcription of the target gene.

Conclusions

We developed a microinjection system for RNAi studies in D. pulex. These techniques add to the growing genomic toolbox and enhance the genetic tractability of this important model for environmental, evolutionary, and developmental genomics.

Lentiviral vector-mediated RNA silencing in the central nervous system

RNA silencing is an established method for investigating gene function and has attracted particular interest because of the potential for generating RNA-based therapeutics. Using lentiviral vectors as an efficient delivery system that offers stable, long-term expression in postmitotic cells further enhances the applicability of an RNA-based gene therapy for the CNS. In this review we provide an overview of both lentiviral vectors and RNA silencing along with design considerations for generating lentiviral vectors capable of RNA silencing. We go on to describe the current preclinical data regarding lentiviral vector-mediated RNA silencing for CNS disorders and discuss the concerns of side effects associated with lentiviral vectors and small interfering RNAs and how these might be mitigated.

Optimisation of tomato Micro-tom regeneration and selection on glufosinate/Basta and dependency of gene silencing on transgene copy number

An efficient protocol of transformation and selection of transgenic lines of Micro-tom, a widespread model cultivar for tomato, is reported. RNA interference silencing efficiency and stability have been investigated and correlated with the number of insertions. Given its small size and ease of cultivation, the tomato (Solanum lycopersicon) cultivar Micro-tom is of widespread use as a model tomato plant. To create and screen transgenic plants, different selectable markers are commonly used. The bar marker carrying the resistance to the herbicide glufosinate/Basta, has many advantages, but it has been little utilised and with low efficiency for identification of tomato transgenic plants. Here we describe a procedure for accurate selection of transgenic Micro-tom both in vitro and in soil. Immunoblot, Southern blot and phenotypic analyses showed that 100 % of herbicide-resistant plants were transgenic. In addition, regeneration improvement has been obtained by using 2 mg/l Gibberellic acid in the shoot elongation medium; rooting optimisation on medium containing 1 mg/l IAA allowed up to 97 % of shoots developing strong and very healthy roots after only 10 days. Stable transformation frequency by infection of leaf explants with Agrobacterium reached 12 %. Shoots have been induced by combination of 1 mg/l zeatin-trans and 0.1 mg/l IAA. Somatic embryogenesis of cotyledon on medium containing 1 mg/l zeatin + 2 mg/l IAA is described in Micro-tom. The photosynthetic psbS gene has been used as reporter gene for RNA silencing studies. The efficiency of gene silencing has been found equivalent using three different target gene fragments of 519, 398 and 328 bp. Interestingly, silencing efficiency decreased from T0 to the T3 generation in plants containing multiple copies of the inserted T-DNA, while it was stable in plants containing a single insertion.

Effects of RNA interference-mediated knock-down of hypoxia-inducible factor-α on respiratory burst activity of the Pacific oyster Crassostrea gigas hemocytes

In mammals, hypoxia-inducible factor-1 α (HIF-1α) is known to play important roles not only in oxygen homeostasis but also in innate immune responses. In this study, to assess the functional role of HIF-α in respiratory burst activity of Crassostrea gigas hemocytes, oysters were injected with HIF-α- or green fluorescent protein (GFP)-targeted-long double-stranded RNAs (dsRNAs), and at 1, 3, and 7 days post-injection, knock-down of C. gigas HIF-α expression and production of reactive oxygen species (ROS) were analyzed. Expression of HIF-α in mantle, gill, and hemocytes of C. gigas was clearly down-regulated by injection of the HIF-α-targeted-long dsRNA, but was not inhibited by the GFP-targeted-long dsRNA, indicating that HIF-α expression was suppressed through sequence-specific and systemic RNA interference (RNAi). Respiratory burst activity of hemocytes was significantly increased by administration of GFP-targeted-long dsRNA. However, knock-down of HIF-α expression led to significant decrease of chemiluminescence (CL) response of C. gigas hemocytes at 3 and 7 days post-administration of HIF-α-targeted-long dsRNA, indicating the critical role of HIF-α in activation of respiratory burst activity of oyster hemocytes.

An injectable cell penetrable nano-polyplex hydrogel for localized siRNA delivery

An approach for application of cell penetration to selective small interference RNA (siRNA) localized delivery system, cell penetrable nano-polyplex assembled hydrogel system, is presented. The cell penetrable nano-polyplex assembled hydrogelisprepared by protamine conjugation to poly(organophos-phazene) and inducement of nano-polyplexes with siRNAs. After an injection of cell penetrable nano-polyplex solution into the body, it turns into a gel due to thermosensitivity of poly(organo- phosphazene). The gel maintains up to 4 weeks and the released 30 nm-sized nano-polyplexes from the gel induces highly effective siRNA delivery due to cell penetration. Accordingly, the new system shows a high gene silencing efficiency on only the target site in long-term with a single injection.

Delivery of dsRNA for RNAi in insects: an overview and future directions

RNA interference (RNAi) refers to the process of exogenous double-stranded RNA (dsRNA) silencing the complementary endogenous messenger RNA. RNAi has been widely used in entomological research for functional genomics in a variety of insects and its potential for RNAi-based pest control has been increasingly emphasized mainly because of its high specificity. This review focuses on the approaches of introducing dsRNA into insect cells or insect bodies to induce effective RNAi. The three most common delivery methods, namely, microinjection, ingestion, and soaking, are illustrated in details and their advantages and limitations are summarized for purpose of feasible RNAi research. In this review, we also briefly introduce the two possible dsRNA uptake machineries, other dsRNA delivery methods and the history of RNAi in entomology. Factors that influence the specificity and efficiency of RNAi such as transfection reagents, selection of dsRNA region, length, and stability of dsRNA in RNAi research are discussed for further studies.

Lentiviral vectors encoding short hairpin RNAs efficiently transduce and knockdown LINGO-1 but induce an interferon response and cytotoxicity in central nervous system neurones

BACKGROUND

Knocking down neuronal LINGO-1 using short hairpin RNAs (shRNAs) might enhance axon regeneration in the central nervous system (CNS). Integration-deficient lentiviral vectors have great potential as a therapeutic delivery system for CNS injuries. However, recent studies have revealed that shRNAs can induce an interferon response resulting in off-target effects and cytotoxicity.

METHODS

CNS neurones were transduced with integration-deficient lentiviral vectors in vitro. The transcriptional effect of shRNA expression was analysed using quantitative real time-polymerase chain reaction and northern blots were used to assess shRNA production.

RESULTS

Integration-deficient lentiviral vectors efficiently transduced CNS neurones and knocked down LINGO-1 mRNA in vitro. However, an increase in cell death was observed when lentiviral vectors encoding an shRNA were applied or when high vector concentrations were used. We demonstrate that high doses of vector or the use of vectors encoding shRNAs can induce an up-regulation of interferon-stimulated genes (2',5'-oligoadenylate synthase 1 and protein kinase R although not myxovirus resistance 1) and a down-regulation of off-target genes (including p75(NTR) and Nogo receptor 1). Furthermore, the northern blot demonstrated that these negative consequences occur even when lentiviral vectors express low levels of shRNAs. Taken together, these results may explain why neurite outgrowth was not enhanced on an inhibitory substrate following transduction with lentiviral vectors encoding an shRNA targeting LINGO-1.

CONCLUSIONS

These findings highlight the importance of including appropriate controls to verify silencing specificity and the requirement to check for an interferon response when conducting RNA interference experiments. However, the potential benefits that RNA interference and viral vectors offer to gene-based therapies to CNS injuries cannot be overlooked and demand further investigation.