Disruption of amylase genes by RNA interference affects reproduction in the Pacific oyster Crassostrea gigas

Feeding strategies and digestive capacities can have important implications for variation in energetic pathways associated with ecological and economically important traits, such as growth or reproduction in bivalve species. Here, we investigated the role of amylase in the digestive processes of Crassostrea gigas, using in vivo RNA interference. This approach also allowed us to investigate the relationship between energy intake by feeding and gametogenesis in oysters. Double-stranded (ds)RNA designed to target the two α-amylase genes A and B was injected in vivo into the visceral mass of oysters at two doses. These treatments caused significant reductions in mean mRNA levels of the amylase genes: −50.7% and −59% mRNA A, and −71.9% and −70.6% mRNA B in 15 and 75 µg dsRNA-injected oysters, respectively, relative to controls. Interestingly, reproductive knock-down phenotypes were observed for both sexes at 48 days post-injection, with a significant reduction of the gonad area (−22.5% relative to controls) and germ cell under-proliferation revealed by histology. In response to the higher dose of dsRNA, we also observed reductions in amylase activity (−53%) and absorption efficiency (−5%). Based on these data, dynamic energy budget modeling showed that the limitation of energy intake by feeding that was induced by injection of amylase dsRNA was insufficient to affect gonadic development at the level observed in the present study. This finding suggests that other driving mechanisms, such as endogenous hormonal modulation, might significantly change energy allocation to reproduction, and increase the maintenance rate in oysters in response to dsRNA injection.

Toward an effective strategy in glioblastoma treatment. Part II: RNA interference as a promising way to sensitize glioblastomas to temozolomide.

International audience

Investigation of the functional roles of host cell proteins involved in Coronavirus infection using highly specific and scalable RNA interference (RNAi) approach

Since its identification in the 1990s, the RNA interference (RNAi) pathway has proven extremely useful in elucidating the function of proteins in the context of cells and even whole organisms. In particular, this sequence-specific and powerful loss-of-function approach has greatly simplified the study of the role of host cell factors implicated in the life cycle of viruses. Here, we detail the RNAi method we have developed and used to specifically knock down the expression of ezrin, an actin binding protein that was identified by yeast two-hybrid screening to interact with the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) spike (S) protein. This method was used to study the role of ezrin, specifically during the entry stage of SARS-CoV infection.

RNA interference technology as a potential control method for fruit and horticultural crops pathogens Botrytis cinerea and Plasmopara viticola

Chapter 1, a general introduction on Botrytis cinerea and its threat to crop production is presented. What Botrytis looks like, its life cycle, why it is a threat to agricultural production, its worldwide pest status, and its current state of management is further elaborated on. Chapter 2, a general introduction on Plasmopara viticola, its threat to grape production and management strategies presented. Chapter 3, titled " RNA Interference Strategies for Future Management of Plant Pathogenic Fungi: Prospects and Challenges ", presents the rapid improvement and extensive implementation of RNA interference (RNAi) technology for the management of fungal pathogens. In this chapter, we describe the application of exogenous RNAi involved in plant pathogenic fungi and discuss dsRNA production, formulation, and RNAi delivery methods. Chapter 4, titled " Exogenous dsRNAs against chitin synthase and glucan synthase genes suppress the growth of the pathogenic fungus Botrytis cinerea " addresses two important questions: Is RNAi technology functional for B. cinerea control ? And which target genes can be exploited for RNAi-based B.cinerea disease control ? Upon target genes selections, an exogenous RNAi protocol was set up and we could effectively deliver a known dose of bacterially produced double stranded RNA (dsRNA) to induce RNAi in B. cinerea. Chapter 5, titled " Double-Stranded RNA Targeting Dicer-Like Genes Compromises the Pathogenicity of Plasmopara viticola on Grapevine “, which deals mainly on RNAi induction against Plasmopara viticola. This chapter addresses two main questions: Is RNAi technology functional in contrasting Plasmopara viticola? And which target genes can be exploited for RNAi-based disease control in Plasmopara viticola?. In the last Chapter (Chapter 6) titled “General discussions and perspectives for future research”, the major research findings from this thesis are discussed together with perspectives for future research.

Inhibition of Expression of HTLV-1 Structural Genes Mediated by Short Hairpin RNA In Vitro

Background: Human T-lymphotropic virus 1 (HTLV-1) is associated with the T-cell malignancy known as adult T-cell leukemia! lymphoma (ATLL) and with a disorder called HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Currently, the treatment of these diseases is based on symptom relief. RNA interference (RNAi) technology has been described as an efficient mechanism for development of new therapeutic methods. Thus, the aim of this study was to evaluate the inhibition of HTLV-1 structural proteins using short hairpin RNAs (shRNAs) expressed by non-viral vectors. Materials and Methods: Reporter plasmids that express enhanced green fluorescent protein-Gag (EGFP-Gag) and EGFP-Env fusion proteins and vectors that express shRNAs corresponding to the HTLV-1 gag and env genes were constructed. shRNA vectors and reporter plasmids were simultaneously transfected into HEK 293 cells. Results: Fluorescence microscopy, flow cytometry and real-time PCR showed that shRNAs were effective in inhibiting the fusion proteins. Conclusion: These shRNAs are effective against the expression of structural genes and may provide an approach to the development of new therapeutic agents.

Involvement of the RNA-binding protein ARE/poly(U)-binding factor 1 (AUF1) in the cytotoxic effects of proinflammatory cytokines on pancreatic beta cells.

AIMS/HYPOTHESIS: Chronic exposure of pancreatic beta cells to proinflammatory cytokines leads to impaired insulin secretion and apoptosis. ARE/poly(U)-binding factor 1 (AUF1) belongs to a protein family that controls mRNA stability and translation by associating with adenosine- and uridine-rich regions of target messengers. We investigated the involvement of AUF1 in cytokine-induced beta cell dysfunction. METHODS: Production and subcellular distribution of AUF1 isoforms were analysed by western blotting. To test for their role in the control of beta cell functions, each isoform was overproduced individually in insulin-secreting cells. The contribution to cytokine-mediated beta cell dysfunction was evaluated by preventing the production of AUF1 isoforms by RNA interference. The effect of AUF1 on the production of potential targets was assessed by western blotting. RESULTS: MIN6 cells and human pancreatic islets were found to produce four AUF1 isoforms (p42>p45>p37>p40). AUF1 isoforms were mainly localised in the nucleus but were partially translocated to the cytoplasm upon exposure of beta cells to cytokines and activation of the ERK pathway. Overproduction of AUF1 did not affect glucose-induced insulin secretion but promoted apoptosis. This effect was associated with a decrease in the production of the anti-apoptotic proteins, B cell leukaemia/lymphoma 2 (BCL2) and myeloid cell leukaemia sequence 1 (MCL1). Silencing of AUF1 isoforms restored the levels of the anti-apoptotic proteins, attenuated the activation of the nuclear factor-κB (NFκB) pathway, and protected the beta cells from cytokine-induced apoptosis. CONCLUSIONS/INTERPRETATION: Our findings point to a contribution of AUF1 to the deleterious effects of cytokines on beta cell functions and suggest a role for this RNA-binding protein in the early phases of type 1 diabetes.

A rice cis-natural antisense RNA acts as a translational enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness.

cis-natural antisense transcripts (cis-NATs) are widespread in plants and are often associated with downregulation of their associated sense genes. We found that a cis-NAT positively regulates the level of a protein critical for phosphate homeostasis in rice (Oryza sativa). PHOSPHATE1;2 (PHO1;2), a gene involved in phosphate loading into the xylem in rice, and its associated cis-NATPHO1;2 are both controlled by promoters active in the vascular cylinder of roots and leaves. While the PHO1;2 promoter is unresponsive to the plant phosphate status, the cis-NATPHO1;2 promoter is strongly upregulated under phosphate deficiency. Expression of both cis-NATPHO1;2 and the PHO1;2 protein increased in phosphate-deficient plants, while the PHO1;2 mRNA level remained stable. Downregulation of cis-NATPHO1;2 expression by RNA interference resulted in a decrease in PHO1;2 protein, impaired the transfer of phosphate from root to shoot, and decreased seed yield. Constitutive overexpression of NATPHO1;2 in trans led to a strong increase of PHO1;2, even under phosphate-sufficient conditions. Under all conditions, no changes occurred in the level of expression, sequence, or nuclear export of PHO1;2 mRNA. However, expression of cis-NATPHO1;2 was associated with a shift of both PHO1;2 and cis-NATPHO1;2 toward the polysomes. These findings reveal an unexpected role for cis-NATPHO1;2 in promoting PHO1;2 translation and affecting phosphate homeostasis and plant fitness.

Suppression of short interfering RNA-mediated gene silencing by the structural proteins of hepatitis C virus.

Viruses have evolved strategies to overcome the antiviral effects of the host at different levels. Besides specific defence mechanisms, the host responds to viral infection via the interferon pathway and also by RNA interference (RNAi). However, several viruses have been identified that suppress RNAi. We addressed the question of whether hepatitis C virus (HCV) suppresses RNAi, using cell lines constitutively expressing green fluorescent protein (GFP) and inducibly expressing HCV proteins. It was found that short interfering RNA-mediated GFP gene silencing was inhibited when the entire HCV polyprotein was expressed. Further studies showed that HCV structural proteins, and in particular envelope protein 2 (E2), were responsible for this inhibition. Co-precipitation assays demonstrated that E2 bound to Argonaute-2 (Ago-2), a member of the RNA-induced silencing complex, RISC. Thus, HCV E2 that interacts with Ago-2 is able to suppress RNAi.

(A) Optimization of solid body phase synthesis of RNA using the Cpep chemistry. (B) Synthesis of BODIPY labeled oligonucleotides

(A) Solid phase synthesis of oligonucleotides are well documented and are extensively studied as the demands continue to rise with the development of antisense, anti-gene, RNA interference, and aptamers. Although synthesis of RNA sequences faces many challenges, most notably the choice of the 2' -hydroxy protecting group, modified 2' -O-Cpep protected ribonucleotides were synthesized as alternitive building blocks. Altering phosphitylation procedures to incorporate 3' -N,N-diethyl phosphoramidites enhanced the overall reactivity, thus, increased the coupling efficiency without loss of integrety. Furthermore, technical optimizations of solid phase synthesis cycles were carried out to allow for successful synthesis of a homo UIO sequences with a stepwise coupling efficiency reaching 99% and a final yield of 91 %. (B) Over the past few decades, dipyrrometheneboron difluoride (BODIPY) has gained recognition as one of the most versatile fluorophores. Currently, BODIPY labeling of oligonucleotides are carried out post-synthetically and to date, there lacks a method that allows for direct incorporation of BODIPY into oligonucleotides during solid phase synthesis. Therefore, synthesis of BODIPY derived phosphoramidites will provide an alternative method in obtaining fluorescently labelled oligonucleotides. A method for the synthesis and incorporation of the BODIPY analogues into oligonucleotides by phosphoramidite chemistry-based solid phase DNA synthesis is reported here. Using this approach, BODIPY-labeled TlO homopolymer and ISIS 5132 were successfully synthesized.

Artificial micro RNA system in Dictyostelium discoideum

Dictyostelium discoideum is a social amoeba that serves as a model system for RNA interference and related mechanisms. Its position between plants and animals enables evolutionary snapshot of mechanisms and protein machinery involved in investigated subjects. MiRNAs are small regulatory RNAs that are evolutionary conserved and present in animals, plants, viruses and some prokaryotes. They have roles in development, cell growth and differentiation, apoptosis and their miss-regulation is associated with many diseases such as cancer, neurodegenerative disorders and diabetes. Recently, through sequencing of DNA libraries miRNAs have been discovered in D. discoideum. In this work, it has been shown that heterologues miRNA let-7 can be expressed and processed in D. discoideum. Expression of let-7 miRNA in social amoeba resulted in a strong developmental phenotype suggesting an overload of the processing/silencing system or/and endogenous targets. The various effects on prel-7 strain have been observed and characterized, serving as a background for postulation of miRNA roles. An artificial miRNA system has been established and imposed to D. discoideum, showing that miRNAs in Dictyostelium could mediate gene expression on the level of mRNA stability and on the posttranscriptional level. Furthermore, presence of translational inhibition as a type of gene control was shown for the first time in this organism. Due to it new structures representing co-localities of miRNA and target mRNA have been detected. Taken together, this work shows functional artificial miRNA system and postulates roles of endogenous small RNA in social amoeba.

HelF und sein Interaktionspartner Xrn1: zwei Regulatoren der RNA-Interferenz in D. discoideum

Hauptziel dieser Arbeit ist die Identifizierung, Verifizierung und Charakterisierung von Interaktionspartnern von HelF, einem Negativregulator der RNA-Interferenz in Dictyostelium discoideum (Popova et al. 2006). Es ist gelungen, die Interaktion von HelF und der 5‘ 3‘ Exonuklease Xrn1 nachzu-weisen, aber alle anderen Versuchen, bisher unbekannte Protein-Interaktionspartner zu identifizieren, schlugen fehl. Xrn1 ist in den Organismen D. melanogaster (Orban und Izaurralde 2005), C. elegans (Newbury und Woollard 2004) und A. thaliana (Gazzani et al. 2004) bereits als Regulator der RNA-Interferenz bekannt. Mit Aufreinigungen nach der TAP-Methode und mit dem Nanotrap wurde ebenfalls versucht, RNA-Interaktionspartner von HelF zu identifizieren. Es konnten in einigen Aufreinigungen putative, für HelF spezifische RNAs identifiziert werden, doch entweder es handelte sich nachweislich nicht um RNA oder die Reproduktion der Daten schlug trotz mehrfacher Versuche fehl. Bezüglich der zellulären Lokalisation von HelF und Xrn1 konnte gezeigt werden, dass HelF zusätzlich zur bekannten Lokalisation in Foci im Nukleus (Popova et al. 2006) vermutlich auch im Cytoplasma und dort angeordnet in mehreren Granula zu finden ist. Xrn1 ist nahezu ausschließlich im Cytoplasma lokalisiert, wo es in mehreren Foci organisiert ist. Es wird vermutet, dass es sich bei diesen Foci um Processing-Bodies (P-Bodies) handelt und dass möglicherweise Xrn1 und HelF in eben diesen P-Bodies co-lokalisieren. In der Entwicklung vom Einzeller zum mehrzelligen Organismus zeigen die Xrn1KO- und die HelFKO-Mutante jeweils einen eindeutigen Phänotyp, der vom Wildtyp abweicht. Die Phänotypen der beiden Mutanten unterscheiden sich deutlich voneinander. Beim Mischen von HelF-Knockout-Zellen mit grün fluoreszierenden Wildtyp-Zellen zeigt sich, dass beide Stämme innerhalb des sich entwickelnden Organismus an definierten Stellen lokalisieren. Entgegen den Erwartungen befinden sich die Zellen der Mutante in den Stadien „Finger“ und „Slug“ nicht hauptsächlich im vorderen Teil des Organismus, sondern sind auch im hinteren Teil, der später die Sporenmasse bildet, vertreten. Dies lässt vermuten, dass HelF-Knockout-Mutanten in gleichem Maße wie Wildtypzellen als Sporen in die nächste Generation übergehen. Weitere Mix-Experimente, in denen HelFKO-Zellen und Xrn1KO-Zellen mit grün fluoreszierenden Wildtypzellen gemischt wurden, belegen eindeutig, dass beide Knockoutmutanten in Konkurrenz zum Wildtyp bei der Generierung von Sporen und somit beim Übergang in die nächste Generation benachteiligt sind. Dies steht im Gegensatz zu den Ergebnissen der vorher beschriebenen Mix-Experimente, in denen der Organismus als Ganzes betrachtet wurde. Weiterhin konnte herausgefunden werden, dass Xrn1 ebenso wie HelF (Popova et al. 2006) eine Rolle als Negativregulator in der RNA-Interferenz innehat. Fraglich ist aber, ob HelF wie bisher angenommen auch Einfluss auf den Weg der Generierung von miRNAs nimmt, da in HelFKO für keinen der beiden miRNA-Kandidaten eine Hoch- bzw. Runterregulierung der reifen miRNAs im Vergleich zum Wildtyp beobachtet werden kann. Im Xrn1KO hingegen ist die reife miRNA ddi-mir-1176 im Vergleich zum Wildtyp hochreguliert. In Bezug auf die Generierung von siRNAs konnte herausgefunden werden, dass Xrn1 und HelF im Fall der Generierung von Skipper siRNAs regulierend eingreifen, dass aber nicht alle siRNAs von der negativen Regulierung durch HelF und Xrn1betroffen sind, was am Beispiel der DIRS-1-siRNAs belegt werden kann. Das von B. Popova entwickelte Modell (Popova 2005) bezüglich der Rolle von HelF in der RNA-Interferenz wurde basierend auf den neu gewonnenen Daten weiterentwickelt und um Xrn1 ergänzt, um die Funktionen von HelF und Xrn1 als Antagonisten der RNA-Interferenz näher zu beleuchten. Literatur: Gazzani, S., T. Lawrenson, et al. (2004). "A link between mRNA turnover and RNA interference in Arabidopsis." Science 306(5698): 1046-8. Newbury, S. and A. Woollard (2004). "The 5'-3' exoribonuclease xrn-1 is essential for ventral epithelial enclosure during C. elegans embryogenesis." Rna 10(1): 59-65. Orban, T. I. and E. Izaurralde (2005). "Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome." Rna 11(4): 459-69. Popova, B. (2005). HelF, a suppressor of RNAi mediated gene silencing in Dictyostelium discoideum. Genetik. Kassel, Universität Kassel. PhD: 200. Popova, B., M. Kuhlmann, et al. (2006). "HelF, a putative RNA helicase acts as a nuclear suppressor of RNAi but not antisense mediated gene silencing." Nucleic Acids Res 34(3): 773-84.

Disruption of vitellogenin gene function in adult honeybees by intra-abdominal injection of double-stranded RNA

Abstract Background The ability to manipulate the genetic networks underlying the physiological and behavioural repertoires of the adult honeybee worker (Apis mellifera) is likely to deepen our understanding of issues such as learning and memory generation, ageing, and the regulatory anatomy of social systems in proximate as well as evolutionary terms. Here we assess two methods for probing gene function by RNA interference (RNAi) in adult honeybees. Results The vitellogenin gene was chosen as target because its expression is unlikely to have a phenotypic effect until the adult stage in bees. This allowed us to introduce dsRNA in preblastoderm eggs without affecting gene function during development. Of workers reared from eggs injected with dsRNA derived from a 504 bp stretch of the vitellogenin coding sequence, 15% had strongly reduced levels of vitellogenin mRNA. When dsRNA was introduced by intra-abdominal injection in newly emerged bees, almost all individuals (96 %) showed the mutant phenotype. An RNA-fragment with an apparent size similar to the template dsRNA was still present in this group after 15 days. Conclusion Injection of dsRNA in eggs at the preblastoderm stage seems to allow disruption of gene function in all developmental stages. To dissect gene function in the adult stage, the intra-abdominal injection technique seems superior to egg injection as it gives a much higher penetrance, it is much simpler, and it makes it possible to address genes that are also expressed in the embryonic, larval or pupal stages.

Trypanosoma brucei RRM1 is a nuclear RNA-binding protein and modulator of chromatin structure

TbRRM1 of Trypanosoma brucei is a nucleoprotein that was previously identified in a search for splicing factors in T. brucei. We show that TbRRM1 associates with mRNAs and with the auxiliary splicing factor polypyrimidine tract-binding protein 2, but not with components of the core spliceosome. TbRRM1 also interacts with several retrotransposon hot spot (RHS) proteins and histones. RNA immunoprecipitation of a tagged form of TbRRM1 from procyclic (insect) form trypanosomes identified ca. 1,500 transcripts that were enriched and 3,000 transcripts that were underrepresented compared to cellular mRNA. Enriched transcripts encoded RNA-binding proteins, including TbRRM1 itself, several RHS transcripts, mRNAs with long coding regions, and a high proportion of stage-regulated mRNAs that are more highly expressed in bloodstream forms. Transcripts encoding ribosomal proteins, other factors involved in translation, and procyclic-specific transcripts were underrepresented. Knockdown of TbRRM1 by RNA interference caused widespread changes in mRNA abundance, but these changes did not correlate with the binding of the protein to transcripts, and most splice sites were unchanged, negating a general role for TbRRM1 in splice site selection. When changes in mRNA abundance were mapped across the genome, regions with many downregulated mRNAs were identified. Two regions were analyzed by chromatin immunoprecipitation, both of which exhibited increases in nucleosome occupancy upon TbRRM1 depletion. In addition, subjecting cells to heat shock resulted in translocation of TbRRM1 to the cytoplasm and compaction of chromatin, consistent with a second role for TbRRM1 in modulating chromatin structure. IMPORTANCE: Trypanosoma brucei, the parasite that causes human sleeping sickness, is transmitted by tsetse flies. The parasite progresses through different life cycle stages in its two hosts, altering its pattern of gene expression in the process. In trypanosomes, protein-coding genes are organized as polycistronic units that are processed into monocistronic mRNAs. Since genes in the same unit can be regulated independently of each other, it is believed that gene regulation is essentially posttranscriptional. In this study, we investigated the role of a nuclear RNA-binding protein, TbRRM1, in the insect stage of the parasite. We found that TbRRM1 binds nuclear mRNAs and also affects chromatin status. Reduction of nuclear TbRRM1 by RNA interference or heat shock resulted in chromatin compaction. We propose that TbRRM1 regulates RNA polymerase II-driven gene expression both cotranscriptionally, by facilitating transcription and efficient splicing, and posttranscriptionally, via its interaction with nuclear mRNAs.

RNA: Networks & imaging

The past few years have brought about a fundamental change in our understanding and definition of the RNA world and its role in the functional and regulatory architecture of the cell. The discovery of small RNAs that regulate many aspects of differentiation and development have joined the already known non-coding RNAs that are involved in chromosome dosage compensation, imprinting, and other functions to become key players in regulating the flow of genetic information. It is also evident that there are tens or even hundreds of thousands of other non-coding RNAs that are transcribed from the mammalian genome, as well as many other yet-to-be-discovered small regulatory RNAs. In the recent symposium RNA: Networks & Imaging held in Heidelberg, the dual roles of RNA as a messenger and a regulator in the flow of genetic information were discussed and new molecular genetic and imaging methods to study RNA presented.

Nanomolar Levels Of Pahs In Extracts From Urban Air Induce Mapk Signaling In Hepg2 Cells.

Polycyclic aromatic hydrocarbons (PAHs) are common environmental pollutants that occur naturally in complex mixtures. Many of the adverse health effects of PAHs including cancer are linked to the activation of intracellular stress response signaling. This study has investigated intracellular MAPK signaling in response to PAHs in extracts from urban air collected in Stockholm, Sweden and Limeira, Brazil, in comparison to BP in HepG2 cells. Nanomolar concentrations of PAHs in the extracts induced activation of MEK4 signaling with down-stream increased gene expression of several important stress response mediators. Involvement of the MEK4/JNK pathway was confirmed using siRNA and an inhibitor of JNK signaling resulting in significantly reduced MAPK signaling transactivated by the AP-1 transcription factors ATF2 and c-Jun. ATF2 was also identified as a sensitive stress responsive protein with activation observed at extract concentrations equivalent to 0.1 nM BP. We show that exposure to low levels of environmental PAH mixtures more strongly activates these signaling pathways compared to BP alone suggesting effects due to interactions. Taken together, this is the first study showing the involvement of MEK4/JNK/AP-1 pathway in regulating the intracellular stress response after exposure to nanomolar levels of PAHs in environmental mixtures.