Relevant bibliographies by topics / RNA

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'RNA'

Author: Grafiati
Published: 4 June 2021
Last updated: 16 November 2024

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Journal articles on the topic "RNA"

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OHNO, Hirohisa, and Hirohide SAITO. "RNA/RNP Nanotechnology for Biological Applications." Seibutsu Butsuri 56, no. 1 (2016): 023–26. http://dx.doi.org/10.2142/biophys.56.023.

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SHIROGUCHI, Katsuyuki. "RNA Sequencing." Seibutsu Butsuri 53, no. 6 (2013): 290–94. http://dx.doi.org/10.2142/biophys.53.290.

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Shi, Rui-Zhu, Yuan-Qing Pan, and Li Xing. "RNA Helicase A Regulates the Replication of RNA Viruses." Viruses 13, no. 3 (February 25, 2021): 361. http://dx.doi.org/10.3390/v13030361.

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The RNA helicase A (RHA) is a member of DExH-box helicases and characterized by two double-stranded RNA binding domains at the N-terminus. RHA unwinds double-stranded RNA in vitro and is involved in RNA metabolisms in the cell. RHA is also hijacked by a variety of RNA viruses to facilitate virus replication. Herein, this review will provide an overview of the role of RHA in the replication of RNA viruses.
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Afonin, Kirill A., Mathias Viard, Ioannis Kagiampakis, Christopher L. Case, Marina A. Dobrovolskaia, Jen Hofmann, Ashlee Vrzak, et al. "Triggering of RNA Interference with RNA–RNA, RNA–DNA, and DNA–RNA Nanoparticles." ACS Nano 9, no. 1 (December 18, 2014): 251–59. http://dx.doi.org/10.1021/nn504508s.

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Kim, Hyunjong, and Juhee Ryu. "Mechanism of Circular RNAs and Their Potential as Novel Therapeutic Agents in Retinal Vascular Diseases." Yakhak Hoeji 67, no. 6 (December 31, 2023): 325–34. http://dx.doi.org/10.17480/psk.2023.67.6.325.

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Maintaining and preserving visual function became critical in this aging society. The number of patients with retinal vascular disease such as retinopathy of prematurity, age-related macular degeneration, and diabetic retinopathy is gradually increasing due to increased life expectancy, advancements in the technology of delivering premature babies, and complications due to eating habits. To treat these retinal vascular diseases, surgical intervention such as laser photocoagulation and anti-vascular endothelial growth factor (VEGF) drugs can be considered. However, these treatment options are accompanied by various complications and adverse effects. Thus, new treatments focusing on the pathogenesis of retinal vascular disease need to be developed. Various evidences suggest that circular RNA is involved in the pathogenesis of retinal disease. In this article, we discuss about currently used treatments of retinal vascular diseases and the emerging role of circular RNAs in the pathogenesis of retinal vascular diseases. Therefore, understanding the mechanism of circular RNA regulating retinal disease and developing therapeutics using these circular RNAs may offer novel treatment options to cure retinal vascular disease.
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Rajkowitsch, Lukas, Doris Chen, Sabine Stampfl, Katharina Semrad, Christina Waldsich, Oliver Mayer, Michael F. Jantsch, Robert Konrat, Udo Bläsi, and Renée Schroeder. "RNA Chaperones, RNA Annealers and RNA Helicases." RNA Biology 4, no. 3 (July 2007): 118–30. http://dx.doi.org/10.4161/rna.4.3.5445.

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Sengoku, T., O. Nureki, and S. Yokoyama. "Structural basis for RNA translocation by RNA helicase." Seibutsu Butsuri 43, supplement (2003): S98. http://dx.doi.org/10.2142/biophys.43.s98_2.

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Tang, Lin. "Mapping RNA–RNA interactions." Nature Methods 17, no. 8 (July 31, 2020): 760. http://dx.doi.org/10.1038/s41592-020-0922-9.

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Ligoxygakis, P. "RNA that synthesizes RNA." Trends in Genetics 17, no. 7 (July 1, 2001): 380. http://dx.doi.org/10.1016/s0168-9525(01)02391-5.

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Ogasawara, Shinzi, and Ai Yamada. "RNA Editing with Viral RNA-Dependent RNA Polymerase." ACS Synthetic Biology 11, no. 1 (January 3, 2022): 46–52. http://dx.doi.org/10.1021/acssynbio.1c00332.

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Dissertations / Theses on the topic "RNA"

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Warner, Katherine Deigan. "Structural studies of small molecule-RNA interactions in druggable RNA targets and fluorogenic RNAs." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708889.

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Hall, Adam. "Biogenesis of Y RNA-derived small RNAs." Thesis, University of East Anglia, 2013. https://ueaeprints.uea.ac.uk/42404/.

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Small non-coding RNAs (sRNAs) constitute a significant portion of the transcriptome in eukaryotes. Many of these sRNAs regulate gene expression. Next-generation sequencing (NGS) has revealed a plethora of previously uncharacterised sRNAs with potential biological function, a number of which originate from longer RNAs. Here, the biogenesis of sRNAs derived from the non-coding Y RNAs (YsRNAs) was characterised as a model for understanding this emerging class of sRNA fragments. Y RNAs are highly conserved, 100 nt long molecules involved in DNA replication which bind to the autoimmune proteins Ro60 and La. YsRNAs are produced in cells undergoing apoptosis. Here, it was demonstrated that YsRNAs are generated from the 5’ and 3’ ends of all four Y RNAs in stressed and unstressed cells. Furthermore, production of these fragments was observed in both cancerous and non-cancerous cells. Although YsRNAs have been proposed to have gene silencing activity, experiments done here found that YsRNAs do not enter the microRNA pathway and are not generated by the gene silencing-related protein Dicer. Furthermore, experiments established that the enzyme which produces fragments from tRNAs, angiogenin, was also not responsible for YsRNA generation. Using mammalian cultured cells along with gene knockout and RNA interference (RNAi) technology, it was determined that RNase L contributed to YsRNA generation. Furthermore, the Y RNA binding protein Ro60 was shown to be essential for YsRNA production through a model of RNase protection. Analysis of deep sequencing data in Ro60 knockout cells revealed that many other sRNAs are also dependent on Ro60. Finally, a ‘high definition’ (HD) protocol to improve NGS detection of sRNAs was tested. The HD protocol was found to be better at detecting sRNAs than current methods. This will facilitate more efficient detection of novel sRNAs in the future.
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Richter, Andreas S. [Verfasser], and Rolf [Akademischer Betreuer] Backofen. "Computational analysis and prediction of RNA-RNA interactions = Computergestützte Analyse und Vorhersage von RNA-RNA-Interaktionen." Freiburg : Universität, 2012. http://d-nb.info/1123475695/34.

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Garbutt, Jennifer S. "RNA interference in insects : persistence and uptake of double-stranded RNA and activation of RNAi genes." Thesis, University of Bath, 2011. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.548101.

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RNA interference (RNAi) is a eukaryotic phenomenon where short double-stranded RNA molecules (dsRNAs) repress homologous sequences. In insects RNAi has been widely observed and has proved extremely useful as a reverse genetics tool to elucidate the function of newly identified genes, as well as showing potential as a novel insecticide. Unfortunately, however, not all insect species are equally susceptible to RNAi. This thesis explores whether persistence of dsRNA in insect hemolymph, uptake of dsRNA into insect tissue, or activation of RNAi genes could be limiting factors in RNAi experiments. Trials were conducted with the tobacco hornworm, Manduca sexta, a species in which experimental difficulty has been experienced with RNAi protocols and the German cockroach, Blattella germanica, which is known to be highly susceptible to experimental RNAi. In M. sexta larvae dsRNA disappeared rapidly from the hemolymph in vivo. By comparison, exogenous dsRNA persisted longer in the hemolymph of B. germanica adults. These findings lead me to propose that the rate of persistence of dsRNA in insect hemolymph may be a key factor in determining the susceptibility of insect species to RNAi. Despite such rapid breakdown of dsRNA in M. sexta larvae uptake of exogenous dsRNA into hemocytes, fat body and midgut could be detected by quantitative RT-PCR in vivo and was experimentally investigated in hemocytes in vivo and in vitro using fluorescently labelled dsRNA. Furthermore, quantitative-RT-PCR revealed that the expression of two M. sexta RNAi genes dicer-2 and argonaute-2 (partial sequences of which were isolated during this study) was specifically upregulated in response to injection with dsRNA.
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Wilm, Andreas. "RNA-Alignments und RNA-Struktur in silico." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=979837278.

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Salgado, Maria Paula Santos Cordeiro. "Structural studies of RNA-dependent RNA polymerases." Thesis, Open University, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.430559.

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Lai, Daniel. "Computational analysis of ribonucleic acid basepairs in RNA structure and RNA-RNA interactions." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/57538.

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Ribonucleic acids (RNA), are an essential part of cellular function, transcribed from DNA and translated into protein. Rather than a passive informational medium, RNA can also be highly functional and regulatory. Certain RNAs fold into specific structures giving it enzymatic properties, while others bind to specific targets to guide regulatory processes. With the advent of next-generation sequencing, a large number of novel non-coding RNAs have been discovered through whole-transcriptome sequencing. Many efforts have been made to study the structure and binding partners of these novel RNAs, in order to determine their function and roles. This work begins with a description of my R package R4RNA for manipulating RNA basepair data, the building blocks of RNA structure and RNA binding. The package deals with the input/output and manipulation of RNA basepair and sequence data, along with statistical and visualization methods for evaluation, interpretation and presentation. We also describe R-chie, a visualization tool and web server built on R4RNA that visualizes complex RNA basepairs in conjunction with sequence alignments. We then conduct the largest known evaluation of RNA-RNA interaction methods to date, running state-of-the-art tools on curated experimentally validated datasets. We end with a review of cotranscriptional RNA basepair formation, summarizing biological, theoretical and computational methods for the process, and future directions for improving classical methods in RNA structure prediction. All content chapters of this thesis has been peer-reviewed and published. The work on R4RNA has led to two publications, with the package used to great visual effect by various publications and also adopted by the RNA structure database Rfam. My assessment of RNA-RNA interaction is at present the only published evaluation of its kind, and will hopefully become a benchmark for future tool development and a guide to selecting appropriate tools and algorithms. Our published review on RNA cotranscriptional folding is well-received, being the first review specifically on its topic.
Science, Faculty of
Graduate
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Poolsap, Unyanee. "Computational methods for predictions of RNA pseudoknotted secondary structures and RNA-RNA interactions." 京都大学 (Kyoto University), 2011. http://hdl.handle.net/2433/147348.

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Fritz, Sarah E. "Molecular basis of the DExH-box RNA helicase RNA helicase A (RHA/DHX9) in eukaryotic protein synthesis." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1437413252.

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Pereira, Tiago Campos. "Estudo de possiveis aplicações médicas da interferencia por RNA." [s.n.], 2005. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316861.

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Orientadores: Iscia Teresinha Lopes-Cendes, Ivan de Godoy Maia
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
Made available in DSpace on 2018-08-04T19:04:59Z (GMT). No. of bitstreams: 1 Pereira_TiagoCampos_D.pdf: 3895694 bytes, checksum: d999bfc92e9a2e2c757db34bbfc7d7fa (MD5) Previous issue date: 2005
Doutorado
Genetica Animal e Evolução
Doutor em Genetica e Biologia Molecular
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Books on the topic "RNA"

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Tokkyochō, Japan. RNAi (RNA kanshō). Tōkyō: Tokkyochō, 2006.

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Schmidt, Frank J., ed. RNA-RNA Interactions. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-1896-6.

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Nielsen, Henrik, ed. RNA. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-59745-248-9.

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A, Zimmermann Robert, and Dahlberg Albert E, eds. Ribosomal RNA: Structure, evolution, processing, and function in protein biosynthesis. Boca Raton: CRC Press, 1996.

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Michael, Ladomery, ed. Molecular biology of RNA. Oxford: Oxford University Press, 2011.

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Ross, Engelke David, ed. RNA interference (RNAi): Nuts & bolts of RNAi technology. [Eagleville, PA]: DNA Press, 2003.

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M, Gott Jonatha, ed. RNA modification. San Diego, Calif: Academic Press/Elsevier, 2007.

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Carmichael, Gordon. RNA Silencing. New Jersey: Humana Press, 2005. http://dx.doi.org/10.1385/1592599354.

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Picardi, Ernesto, ed. RNA Bioinformatics. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1307-8.

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McMahon, Mary, ed. RNA Modifications. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1374-0.

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Book chapters on the topic "RNA"

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Merkl, Philipp E., Christopher Schächner, Michael Pilsl, Katrin Schwank, Catharina Schmid, Gernot Längst, Philipp Milkereit, Joachim Griesenbeck, and Herbert Tschochner. "Specialization of RNA Polymerase I in Comparison to Other Nuclear RNA Polymerases of Saccharomyces cerevisiae." In Ribosome Biogenesis, 63–70. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_4.

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AbstractIn archaea and bacteria the major classes of RNAs are synthesized by one DNA-dependent RNA polymerase (RNAP). In contrast, most eukaryotes have three highly specialized RNAPs to transcribe the nuclear genome. RNAP I synthesizes almost exclusively ribosomal (r)RNA, RNAP II synthesizes mRNA as well as many noncoding RNAs involved in RNA processing or RNA silencing pathways and RNAP III synthesizes mainly tRNA and 5S rRNA. This review discusses functional differences of the three nuclear core RNAPs in the yeast S. cerevisiae with a particular focus on RNAP I transcription of nucleolar ribosomal (r)DNA chromatin.
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Cho, B. "RNA–RNA SELEX." In RNA-RNA Interactions, 39–47. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1896-6_3.

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Kwon, Jae-Sung, Raviraj Thakur, Steven T. Wereley, J. David Schall, Paul T. Mikulski, Kathleen E. Ryan, Pamela L. Keating, et al. "RNA Interference (RNAi)." In Encyclopedia of Nanotechnology, 2238. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-90-481-9751-4_100714.

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Leppla, Norman C., Bastiaan M. Drees, Allan T. Showler, John L. Capinera, Jorge E. Peña, Catharine M. Mannion, F. William Howard, et al. "RNA Interference (RNAi)." In Encyclopedia of Entomology, 3195–96. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6359-6_3417.

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Das, Shreya, Chandrani Dey, Santanu Chakraborty, and Arunima Sengupta. "RNA Interference (RNAi)." In Exploring Medical Biotechnology- in vivo, in vitro, in silico, 231–59. Boca Raton: CRC Press, 2024. http://dx.doi.org/10.1201/9781003302131-21.

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Sharma, Sahil, and Cynthia M. Sharma. "Identification of RNA Binding Partners of CRISPR-Cas Proteins in Prokaryotes Using RIP-Seq." In Methods in Molecular Biology, 111–33. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1851-6_6.

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AbstractCRISPR-Cas systems consist of a complex ribonucleoprotein (RNP) machinery encoded in prokaryotic genomes to confer adaptive immunity against foreign mobile genetic elements. Of these, especially the class 2, Type II CRISPR-Cas9 RNA-guided systems with single protein effector modules have recently received much attention for their application as programmable DNA scissors that can be used for genome editing in eukaryotes. While many studies have concentrated their efforts on improving RNA-mediated DNA targeting with these Type II systems, little is known about the factors that modulate processing or binding of the CRISPR RNA (crRNA) guides and the trans-activating tracrRNA to the nuclease protein Cas9, and whether Cas9 can also potentially interact with other endogenous RNAs encoded within the host genome. Here, we describe RIP-seq as a method to globally identify the direct RNA binding partners of CRISPR-Cas RNPs using the Cas9 nuclease as an example. RIP-seq combines co-immunoprecipitation (coIP) of an epitope-tagged Cas9 followed by isolation and deep sequencing analysis of its co-purified bound RNAs. This method can not only be used to study interactions of Cas9 with its known interaction partners, crRNAs and tracrRNA in native systems, but also to reveal potential additional RNA substrates of Cas9. For example, in RIP-seq analysis of Cas9 from the foodborne pathogen Campylobacter jejuni (CjeCas9), we recently identified several endogenous RNAs bound to CjeCas9 RNP in a crRNA-dependent manner, leading to the discovery of PAM-independent RNA cleavage activity of CjeCas9 as well as non-canonical crRNAs. RIP-seq can be easily adapted to any other effector RNP of choice from other CRISPR-Cas systems, allowing for the identification of target RNAs. Deciphering novel RNA-protein interactions for CRISPR-Cas proteins within host bacterial genomes will lead to a better understanding of the molecular mechanisms and functions of these systems and enable us to use the in vivo identified interaction rules as design principles for nucleic acid-targeting applications, fitted to each nuclease of interest.
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Chetverina, Helena V., and Alexander B. Chetverin. "Identifying RNA Recombination Events and Non-covalent RNA–RNA Interactions with the Molecular Colony Technique." In RNA-RNA Interactions, 1–25. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1896-6_1.

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Anupam, R., S. Zhou, and J. V. Hines. "Electrophoretic Mobility Shift Assays: Analysis of tRNA Binding to the T Box Riboswitch Antiterminator RNA." In RNA-RNA Interactions, 135–42. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1896-6_10.

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Zhou, S., R. Anupam, and J. V. Hines. "Fluorescence Anisotropy: Analysis of tRNA Binding to the T Box Riboswitch Antiterminator RNA." In RNA-RNA Interactions, 143–52. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1896-6_11.

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Bak, Geunu, Kook Han, Kwang-sun Kim, and Younghoon Lee. "Electrophoretic Mobility Shift Assay of RNA–RNA Complexes." In RNA-RNA Interactions, 153–63. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1896-6_12.

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Conference papers on the topic "RNA"

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Adamek, Maksimiljan. "Molecular Grammar of RNA-binding Protein Interactions in Formation and Function of Ribonucleoprotein Complexes." In Socratic Lectures 8. University of Lubljana Press, 2023. http://dx.doi.org/10.55295/psl.2023.ii15.

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Ribonucleoproteins (RNPs) are macromolecular assemblies of proteins along RNA molecules to carry out specialized cellular processes. Understanding how RNA binding proteins (RBPs) and RNA sequences determine the interactions to form RNPs and ultimately steer biomolecular processes remains poorly understood. There is a mounting evidence that RNP assembly de-pends on the formation of a network of transient, multivalent RBP RNA and RBP RBP interac-tions, particularly between tyrosine residues from intrinsically disordered domains and argi-nine residues from RNA-binding domains of RBPs. Furthermore, RBPs, especially their intrin-sically disordered regions, are hotspots for posttranslational modification (PTM) sites. Alt-hough PTMs have been well catalogued, little is known about how these modifications regulate RNP assembly and function. Some initial studies introduced the concept of the so-called phos-pho-switch, in which RBPs require phosphorylation for condensation of larger RNP complexes, but it remains unclear how this contributes to the protein function and the pattern of selective protein binding to RNA molecules. This short review will take a look at what is currently known in the field of RNPs, their interactions, and the phase-separated biomolecular conden-sates, which are intimately connected to RNPs and are important for several key cell processes. Keywords: Ribonucleoproteins; RNA binding proteins; Multivalency; Intrinsically disordered proteins; Posttranslational modifications
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Varadarajan, Swetha. "Optimizing RNA-RNA Interaction Computations." In 2019 IEEE/ACM International Symposium on Code Generation and Optimization (CGO). IEEE, 2019. http://dx.doi.org/10.1109/cgo.2019.8661181.

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Bachkova, I. K., S. A. Zhukov, M. S. Kupryushkin, M. A. Zenkova, E. L. Chernolovskaya, and I. V. Chernikov. "THE EFFECT OF MESYL PHOSPHORAMIDATE MODIFICATION ON SIRNA POTENCY IN VITRO." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-295.

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The introduction of chemical modifications into the composition of small interfering RNA (siRNA) improves its biological properties, but can inhibit the RNA interference (RNAi) process. Therefore, in this work, we screened the patterns of modification of siRNAs with mesyl groups (μ), covering 70% of positions in siRNAs. In most positions, μ did not inhibit the RNAi process, so the introduction of μ can potentially improve its biological properties in vivo.
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DOBBS, DRENA, STEVEN E. BRENNER, VASANT G. HONAVAR, ROBERT L. JERNIGAN, ALAIN LAEDERACH, and QUAID MORRIS. "REGULATORY RNA." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2015. http://dx.doi.org/10.1142/9789814749411_0039.

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Techa-angkoon, Prapaporn, and Yanni Sun. "glu-RNA." In BCB'13: ACM-BCB2013. New York, NY, USA: ACM, 2013. http://dx.doi.org/10.1145/2506583.2506617.

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Tsang, Herbert H., and Denny C. Dai. "RNA-DV." In the ACM Conference. New York, New York, USA: ACM Press, 2012. http://dx.doi.org/10.1145/2382936.2383036.

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Cheung, Kwan-Yau, Kwok-Kit Tong, Kin-Hong Lee, and Kwong-Sak Leung. "RIPGA: RNA-RNA interaction prediction using genetic algorithm." In 2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2013. http://dx.doi.org/10.1109/cibcb.2013.6595401.

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Mondal, Chiranjeb, and Sanjay Rajopadhye. "Accelerating the BPMax Algorithm for RNA-RNA Interaction." In 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). IEEE, 2021. http://dx.doi.org/10.1109/ipdpsw52791.2021.00042.

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Kato, Yuki, Tatsuya Akutsu, Hiroyuki Seki, Tuan D. Pham, and Xiaobo Zhou. "A Grammatical Approach to RNA-RNA Interaction Prediction." In COMPUTATIONAL MODELS FOR LIFE SCIENCES/CMLS '07. AIP, 2007. http://dx.doi.org/10.1063/1.2816623.

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Fu, Lingjie, Meili Chen, Jiayan Wu, Jingfa Xiao, and Zhewen Zhang. "Comparative analysis of RNA-seq data from polyA RNAs selection and ribosomal RNAs deletion protocol by strand-specific RNA sequencing technology." In 2014 8th International Conference on Systems Biology (ISB). IEEE, 2014. http://dx.doi.org/10.1109/isb.2014.6990734.

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Reports on the topic "RNA"

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Morris, T. J., and A. O. Jackson. Characterization of defective interfering RNAs associated with RNA plant viruses. Office of Scientific and Technical Information (OSTI), January 1993. http://dx.doi.org/10.2172/6880107.

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Gal-On, Amit, Shou-Wei Ding, Victor P. Gaba, and Harry S. Paris. role of RNA-dependent RNA polymerase 1 in plant virus defense. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597919.bard.

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Objectives: Our BARD proposal on the impact of RNA-dependent RNA polymerase 1 (RDR1) in plant defense against viruses was divided into four original objectives. 1. To examine whether a high level of dsRNA expression can stimulate RDR1 transcription independent of salicylic acid (SA) concentration. 2. To determine whether the high or low level of RDR1 transcript accumulation observed in virus resistant and susceptible cultivars is associated with viral resistance and susceptibility. 3. To define the biogenesis and function of RDR1-dependent endogenous siRNAs. 4. To understand why Cucumber mosaic virus (CMV) can overcome RDR1-dependent resistance. The objectives were slightly changed due to the unique finding that cucumber has four different RDR1 genes. Background to the topic: RDR1 is a key plant defense against viruses. RDR1 is induced by virus infection and produces viral and plant dsRNAs which are processed by DICERs to siRNAs. siRNAs guide specific viral and plant RNA cleavage or serve as primers for secondary amplification of viral-dsRNA by RDR. The proposal is based on our preliminary results that a. the association of siRNA and RDR1 accumulation with multiple virus resistance, and b. that virus infection induced the RDR1-dependent production of a new class of endogenous siRNAs. However, the precise mechanisms underlying RDR1 induction and siRNA biogenesis due to virus infection remain to be discovered in plants. Major conclusions, solutions and achievements: We found that in the cucurbit family (cucumber, melon, squash, watermelon) there are 3-4 RDR1 genes not documented in other plant families. This important finding required a change in the emphasis of our objectives. We characterized 4 RDR1s in cucumber and 3 in melon. We demonstrated that in cucumber RDR1b is apparently a new broad spectrum virus resistance gene, independent of SA. In melon RDR1b is truncated, and therefore is assumed to be the reason that melon is highly susceptible to many viruses. RDR1c is dramatically induced due to DNA and RNA virus infection, and inhibition of RDR1c expression led to increased virus accumulation which suggested its important on gene silencing/defense mechanism. We show that induction of antiviral RNAi in Arabidopsis is associated with production of a genetically distinct class of virus-activated siRNAs (vasiRNAs) by RNA dependent RNA polymerase-1 targeting hundreds of host genes for RNA silencing by Argonaute-2. Production of vasiRNAs is induced by viruses from two different super groups of RNA virus families, targeted for inhibition by CMV, and correlated with virus resistance independently of viral siRNAs. We propose that antiviral RNAi activate broad-spectrum antiviral activity via widespread silencing of host genes directed by vasiRNAs, in addition to specific antiviral defense Implications both scientific and agricultural: The RDR1b (resistance) gene can now be used as a transcription marker for broad virus resistance. The discovery of vasiRNAs expands the repertoire of siRNAs and suggests that the siRNA-processing activity of Dicer proteins may play a more important role in the regulation of plant and animal gene expression than is currently known. We assume that precise screening of the vasiRNA host targets will lead in the near future for identification of plant genes associate with virus diseases and perhaps other pathogens.
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3

Berglund, J. Andrew. RNA Regulation of Estrogen. Fort Belvoir, VA: Defense Technical Information Center, August 2010. http://dx.doi.org/10.21236/ada541794.

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Berglund, J. A., Rodger Voelker, Paul Barber, Julien Diegel, Amy Mahady, and Micah Bodner. RNA Regulation by Estrogen. Fort Belvoir, VA: Defense Technical Information Center, August 2011. http://dx.doi.org/10.21236/ada553263.

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Byrn, Stephen, Nathaniel Milton, and Kari Clase. BIRS Course: RNA Vaccine Manufacture and Assessment of Regulatory Documents for RNA Vaccines. Purdue University, August 2023. http://dx.doi.org/10.5703/1288284317657.

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This paper is in three segments: (A) Segment on Vaccine Manufacture; (B) Segment on Ready to Use (RTU) Fluid Path for Compounded Sterile Preparations, mRNA Vaccines, and Phage Therapy, (C) Segment on Competency Framework for Addressing Regulatory Review These segments can be used separately or in combination. Additionally, they can be presented in any order. The time devoted to each segment depends on the depth of the course coverage. These segments are interrelated and describe how to make vaccines, how to manufacture vaccines with a point-of-care system built from ready-to-use parts; and how to regulate vaccines. This is a timely review because of the importance of vaccines for the treatment of diseases. It is hoped that it will lead to new approaches to vaccine manufacture and regulation.
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Morris, T. J., and A. O. Jackson. Characterization of defective interfering RNAs associated with RNA plant viruses. Progress report. Office of Scientific and Technical Information (OSTI), April 1993. http://dx.doi.org/10.2172/10139870.

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Chakraborty, Srijani. The Dawn of RNA Therapeutics. Spring Library, December 2020. http://dx.doi.org/10.47496/sl.blog.19.

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Turner, Douglas H. Molecular Basis of RNA Catalysis. Fort Belvoir, VA: Defense Technical Information Center, February 1989. http://dx.doi.org/10.21236/ada204745.

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Hubbard, J. Computer modeling 16S ribosomal RNA. Office of Scientific and Technical Information (OSTI), April 1990. http://dx.doi.org/10.2172/6749631.

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Mawassi, Munir, and Valerian Dolja. Role of RNA Silencing Suppression in the Pathogenicity and Host Specificity of the Grapevine Virus A. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592114.bard.

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RNA silencing is a defense mechanism that functions against virus infection and involves sequence-specific degradation of viral RNA. Diverse RNA and DNA viruses of plants encode RNA silencing suppressors (RSSs), which, in addition to their role in viral counterdefense, were implicated in the efficient accumulation of viral RNAs, virus transport, pathogenesis, and determination of the virus host range. Despite rapidly growing understanding of the mechanisms of RNA silencing suppression, systematic analysis of the roles played by diverse RSSs in virus biology and pathology is yet to be completed. Our research was aimed at conducting such analysis for two grapevine viruses, Grapevine virus A (GVA) and Grapevine leafroll-associated virus-2 (GLRaV- 2). Our major achievements on the previous cycle of BARD funding are as follows. 1. GVA and GLRaV-2 were engineered into efficient gene expression and silencing vectors for grapevine. The efficient techniques for grapevine infection resulting in systemic expression or silencing of the recombinant genes were developed. Therefore, GVA and GLRaV-2 were rendered into powerful tools of grapevine virology and functional genomics. 2. The GVA and GLRaV-2 RSSs, p10 and p24, respectively, were identified, and their roles in viral pathogenesis were determined. In particular, we found that p10 functions in suppression and pathogenesis are genetically separable. 3. We revealed that p10 is a self-interactive protein that is targeted to the nucleus. In contrast, p24 mechanism involves binding small interfering RNAs in the cytoplasm. We have also demonstrated that p10 is relatively weak, whereas p24 is extremely strong enhancer of the viral agroinfection. 4. We found that, in addition to the dedicated RSSs, GVA and GLRaV-2 counterdefenses involve ORF1 product and leader proteases, respectively. 5. We have teamed up with Dr. Koonin and Dr. Falnes groups to study the evolution and function of the AlkB domain presents in GVA and many other plant viruses. It was demonstrated that viral AlkBs are RNA-specific demethylases thus providing critical support for the biological relevance of the novel process of AlkB-mediated RNA repair.
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