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Relevant bibliographies by topics / RNA-binding

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Academic literature on the topic 'RNA-binding'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 September 2023

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Journal articles on the topic "RNA-binding"

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Muckstein, U., H. Tafer, J. Hackermuller, S. H. Bernhart, P. F. Stadler, and I. L. Hofacker. "Thermodynamics of RNA-RNA binding." Bioinformatics 22, no. 10 (January 29, 2006): 1177–82. http://dx.doi.org/10.1093/bioinformatics/btl024.

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Hallegger, M., A. Taschner, and M. F. Jantsch. "RNA aptamers binding the double-stranded RNA-binding domain." RNA 12, no. 11 (September 27, 2006): 1993–2004. http://dx.doi.org/10.1261/rna.125506.

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Muto, Yutaka, Chris Oubridge, and Kiyoshi Nagai. "RNA-binding proteins: TRAPping RNA bases." Current Biology 10, no. 1 (January 2000): R19—R21. http://dx.doi.org/10.1016/s0960-9822(99)00250-x.

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Kotelnikov, R. N., S. G. Shpiz, A. I. Kalmykova, and V. A. Gvozdev. "RNA-binding proteins in RNA interference." Molecular Biology 40, no. 4 (July 2006): 528–40. http://dx.doi.org/10.1134/s0026893306040054.

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Serin, Guillaume, Gérard Joseph, Laurence Ghisolfi, Marielle Bauzan, Monique Erard, François Amalric, and Philippe Bouvet. "Two RNA-binding Domains Determine the RNA-binding Specificity of Nucleolin." Journal of Biological Chemistry 272, no. 20 (May 16, 1997): 13109–16. http://dx.doi.org/10.1074/jbc.272.20.13109.

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Sastry, Srin, and Barbara M. Ross. "RNA-binding site in T7 RNA polymerase." Proceedings of the National Academy of Sciences 95, no. 16 (August 4, 1998): 9111–16. http://dx.doi.org/10.1073/pnas.95.16.9111.

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Recent models of RNA polymerase transcription complexes have invoked the idea that enzyme-nascent RNA contacts contribute to the stability of the complexes. Although much progress on this topic has been made with the multisubunit Escherichia coli RNA polymerase, there is a paucity of information regarding the structure of single-subunit phage RNA polymerase transcription complexes. Here, we photo-cross-linked the RNA in a T7 RNA polymerase transcription complex and mapped a major contact site between amino acid residues 144 and 168 and probably a minor contact between residues 1 and 93. These regions of the polymerase are proposed to interact with the emerging RNA during transcription because the 5′ end of the RNA was cross-linked. The contacts are both ionic and nonionic (hydrophobic). The specific inhibitor of T7 transcription, T7 lysozyme, does not compete with T7 RNA polymerase for RNA cross-linking, implying that the RNA does not bind the lysozyme. However, lysozyme may act indirectly via a conformational change in the polymerase. In the current model, the DNA template lies in the polymerase cleft and the fingers subdomain may contact or maintain a template bubble, and a region in the N terminus forms a partly solvent-accessible binding channel for the emerging RNA.

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Singh, Arunima. "RNA-binding protein kinetics." Nature Methods 18, no. 4 (April 2021): 335. http://dx.doi.org/10.1038/s41592-021-01122-6.

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SUGITA, Mamoru, and Masahiro SUGIURA. "Chloroplast RNA-binding Proteins." Nippon Nōgeikagaku Kaishi 71, no. 11 (1997): 1177–79. http://dx.doi.org/10.1271/nogeikagaku1924.71.1177.

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Larochelle, Stéphane. "RNA-binding proteome redux." Nature Methods 16, no. 3 (February 27, 2019): 219. http://dx.doi.org/10.1038/s41592-019-0349-3.

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Laird-Offringa, Ite A., and Joel G. Belasco. "RNA-binding proteins tamed." Nature Structural & Molecular Biology 5, no. 8 (August 1998): 665–68. http://dx.doi.org/10.1038/1356.

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Dissertations / Theses on the topic "RNA-binding"

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Maticzka, Daniel [Verfasser], and Rolf [Akademischer Betreuer] Backofen. "Modelling binding preferences of RNA-binding proteins." Freiburg : Universität, 2017. http://d-nb.info/1135134146/34.

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Khanal, Reecha. "Identification of RNA Binding Proteins and RNA Binding Residues Using Effective Machine Learning Techniques." ScholarWorks@UNO, 2019. https://scholarworks.uno.edu/honors_theses/128.

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Identification and annotation of RNA Binding Proteins (RBPs) and RNA Binding residues from sequence information alone is one of the most challenging problems in computational biology. RBPs play crucial roles in several fundamental biological functions including transcriptional regulation of RNAs and RNA metabolism splicing. Existing experimental techniques are time-consuming and costly. Thus, efficient computational identification of RBPs directly from the sequence can be useful to annotate RBP and assist the experimental design. Here, we introduce AIRBP, a computational sequence-based method, which utilizes features extracted from evolutionary information, physiochemical properties, and disordered properties to train a machine learning method designed using stacking, an advanced machine learning technique, for effective prediction of RBPs. Furthermore, it makes use of efficient machine learning algorithms like Support Vector Machine, Logistic Regression, K-Nearest Neighbor and XGBoost (Extreme Gradient Boosting Algorithm). In this research work, we also propose another predictor for efficient annotation of RBP residues. This RBP residue predictor also uses stacking and evolutionary algorithms for efficient annotation of RBPs and RNA Binding residue. The RNA-binding residue predictor also utilizes various evolutionary, physicochemical and disordered properties to train a robust model. This thesis presents a possible solution to the RBP and RNA binding residue prediction problem through two independent predictors, both of which outperform existing state-of-the-art approaches.

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Deumer, Claudia D. "RNA-binding proteins in yeast mitochondria." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2002. http://nbn-resolving.de/urn:nbn:de:swb:14-1035897639531-83407.

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This work focused on the further characterisation of Idhp and of the Krebs cycle enzymes citrate synthase 1 (Cit1p) and malate dehydrogenase 1 (Mdh1p) both of which have been identified as RNA-binding proteins without known RNA recognition motifs. Besides analysing their effects on mitochondrial translation and their organisation in protein complexes the work focused on the characterisation of the RNA-binding properties of recombinant Cit1p and Mdh1p: · Cit1p and Mdh1p play no essential role in mitochondrial protein synthesis. · Idhp is in a complex of molecular weight larger than the cytochrome c oxidase (250 kDa). · Cit1p and Mdh1p are in mitochondrial complexes smaller than 250 kDa. · 1000-fold molar excess of tRNA referring to COX2 leader RNA did not inhibit the RNA-binding of Cit1p and Mdh1p. · Cit1p and Mdh1p bind mitochondrial mRNAs (sense and antisense). The influence of cofactors and substrates on RNA-binding was analysed in order to reveal a possible link between the enzymatic function and the property of RNA-binding: · Acetyl-CoA and ATP inhibited the RNA-binding of Cit1p and Mdh1p at a concentration of 5 mM.

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Loushin, Newman Carrie Lee. "Characterization of QKI RNA binding function /." Full text (PDF) from UMI/Dissertation Abstracts International, 2000. http://wwwlib.umi.com/cr/utexas/fullcit?p3004323.

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Crombie, Catriona Ann. "Histone hairpin binding protein, an RNA binding protein, essential for development." Thesis, University of Aberdeen, 2003. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU602058.

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Histones are proteins found in the nuclei of eukaryotic cells where they are complexed to DNA in chromatin. Rephcation-dependent histones are expressed only during S-phase. Regulation of expression of replication-dependent histone genes requires a highly conserved hairpin RNA element in the 3' untranslated region of histone mRNAs. Replication-dependent histone mRNAs are not polyadenylated; their 3' end is formed by an endonucleolytic cleavage event, 3' of a hairpin element, which is recognised by the Hairpin Binding Protein, HBP (also known as Stem-Loop Binding Protein, SLBP). This protein-RNA interaction is important for the endonucleolytic cleavage that generates the mature mRNA 3' end. The 3' hairpin, and presumably HBP, are also required for nucleocytoplasmic transport, translation and stability of histone mRNAs. It is therefore important to understand this interaction. The hairpin is highly conserved and I have demonstrated that residues in the hairpin loop are important for binding the HBP. This complimented structural studies that showed that the same residues are involved in stacking interactions in the RNA loop. In cell culture, expression of replication-dependent histone genes is S phase specific as is the expresion of HBP. Here I demonstrated that in Caenorhabditis elegans the HBP promoter is active in dividing cells during embryonic and postembryonic development. Depletion of HBP by RNAi leads to an embryonic lethal phenotype associated with defects in chromosome condensation. Postembryonic depletion of HBP results in defects in cell fate during late larval development, specifically in vulval development. A similar phenotype was obtained when histone H3 and H2A were depleted by RNAi suggesting that the phenotype of the hbp (RNAi) worms was due to a lack of histone proteins. I have confirmed this by showing that histone proteins are indeed reduced in hbp (RNAi) worms. I have also shown that depletion of HBP leads to a change in expression of a number of other proteins and specifically an up-regulation of a histone H3 like protein with an apparent molecular mass of 34 kDa. I have evidence that suggests that this protein is the centromer specific protein, CENP-A. As this protein was up-regulated when RNAi was used to deplete histones proteins, this suggests that there could be a compensatory mechanism that helps the animal to deal with the shortage of histone proteins.

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Whittington, Christi Leigh. "Molecular Dynamics of the RNA Binding Cavity of Influenza A Non-structural Protein 1 (NS1) RNA Binding Domain." Scholar Commons, 2012. http://scholarcommons.usf.edu/etd/4256.

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Molecular dynamics simulations were performed on the influenza A non-structural protein 1 (NS1) RNA binding domain (RBD), a homodimer. Fourteen simulations were performed at 298K, nine ionized with 0.1M KCl and five with no ions. Several analysis techniques were employed to study RBD residue flexibility. The focus of the study was the RNA binding cavity formed by side chains of helix 2 (chain A) and helix 2’ (chain B) and cavity intermonomeric salt bridges. Opening of the salt bridges D29–R46’ and D29’–R46 was observed in several of the trajectories. The RNA binding cavity has large flexibility, where the dimension and shape change during the dynamics. One pair of residues surrounding the cavity and necessary for RNA binding, residues R38 and R38’, have motions during the simulations which cover the top of the cavity. There is correlation between the salt bridge breaking, flexibility of R38 and R38’, and the cavity size and shape changes. Possible RBD small molecule drug targets are these two salt bridges and the pair R38 and R38’. Disrupting the events that occur around these areas could possibly inactivate RNA binding function of the domain. These results could have implications in searching for potential molecules that effectively treat influenza A.

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Blancafort, Pilar. "Making conformation-specific RNA-binding zinc fingers." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0023/NQ47598.pdf.

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Waterman, David Geoffrey. "Structural studies on prokaryotic RNA-binding proteins." Thesis, University of York, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.441058.

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Fesser, Stephanie Marion. "Contribution of RNA binding proteins to substrate specificity in small RNA biogenesis." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-173105.

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Attig, Jan. "Impact of retrotransposon-derived RNA elements and their recognition by RNA binding proteins." Thesis, University of Cambridge, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.709161.

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Books on the topic "RNA-binding"

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Sandberg, Kathryn, and Susan E. Mulroney, eds. RNA Binding Proteins. Boston, MA: Springer US, 2002. http://dx.doi.org/10.1007/978-1-4757-6446-8.

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RNA binding proteins. Austin, Tex: Landes Bioscience, 2012.

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Yeo, Gene W., ed. Systems Biology of RNA Binding Proteins. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1221-6.

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Argonaute proteins: Methods and protocols. New York: Humana Press/Springer, 2011.

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B, Denman Robert, ed. RNA binding proteins in development and disease. Trivandrum: Research Signpost, 2008.

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Symposium on RNA Biology (2nd 1997 North Carolina Biotechnology Center). Symposium on RNA Biology: RNA tool and target : held at North Carolina Biotechnology Center, Research Triangle Park, North Carolina, USA, October 17-19, 1997. [Oxford]: Oxford University Press, 1997.

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Randolph, Lisa Kathryn. Regulation of synapse density by Pumilio RNA-binding proteins. [New York, N.Y.?]: [publisher not identified], 2022.

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Li, Karpra G. P. A structure-function analysis of the smaug RNA-binding domain. Ottawa: National Library of Canada, 2003.

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Ren-Jang, Lin, ed. RNA-protein interaction protocols. 2nd ed. Totowa, N.J: Humana, 2008.

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Ren-Jang, Lin, ed. RNA-protein interaction protocols. 2nd ed. Totowa, N.J: Humana, 2008.

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Book chapters on the topic "RNA-binding"

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Penalva, Luiz O. F. "RNA-binding Protein." In Encyclopedia of Systems Biology, 1875–76. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_313.

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Ritter, Birgit, and Marc R. Reboll. "Purification of RNA-Binding Proteins." In RNA Mapping, 195–201. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1062-5_17.

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Chitsaz, Hamidreza, Rolf Backofen, and S. Cenk Sahinalp. "biRNA: Fast RNA-RNA Binding Sites Prediction." In Lecture Notes in Computer Science, 25–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-04241-6_3.

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Reboll, Marc R. "Mapping of Protein Binding RNA Elements." In RNA Mapping, 187–94. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1062-5_16.

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Zoschke, Reimo, Christiane Kupsch, and Christian Schmitz-Linneweber. "RNA-Binding Proteins Required for Chloroplast RNA Processing." In Plant Mitochondria, 177–203. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-0-387-89781-3_8.

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Jordan, Britta, Lisa Nickel, and Ruth A. Schmitz. "Microscale Thermophoresis to Study RNA–RNA Binding Affinity." In Prokaryotic Gene Regulation, 291–303. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2413-5_15.

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Giudice, Jimena, and Thomas A. Cooper. "RNA-Binding Proteins in Heart Development." In Systems Biology of RNA Binding Proteins, 389–429. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1221-6_11.

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Cole, James L. "RNA-Binding Proteins – Catalytic Domains." In Encyclopedia of Biophysics, 2261–64. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_461.

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Gerstberger, Stefanie, Markus Hafner, Manuel Ascano, and Thomas Tuschl. "Evolutionary Conservation and Expression of Human RNA-Binding Proteins and Their Role in Human Genetic Disease." In Systems Biology of RNA Binding Proteins, 1–55. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1221-6_1.

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Goodwin, Marianne, and Maurice S. Swanson. "RNA-Binding Protein Misregulation in Microsatellite Expansion Disorders." In Systems Biology of RNA Binding Proteins, 353–88. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1221-6_10.

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Conference papers on the topic "RNA-binding"

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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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Huang, Yile, Yulong Qiao, Yu Zhao, Yingzhe Ding, Jie Yuan, Jiajian Zhou, Huating Wang, and Hao Sun. "RNA binding proteins (RBPs) regulate lncRNA nuclear retention." In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2020. http://dx.doi.org/10.1109/bibm49941.2020.9313283.

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Nieves, Bethsaida I., Shuang Niu, Dedeepya Vaka, Julia Salzman, Patrick Brown, and Alejandro I. Sweet-Cordero. "Abstract 204: Molecular function of the RNA binding protein EWS in RNA processing." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-204.

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Deng, Lei, Youzhi Liu, Yechuan Shi, and Hui Liu. "A deep neural network approach using distributed representations of RNA sequence and structure for identifying binding site of RNA-binding proteins." In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2019. http://dx.doi.org/10.1109/bibm47256.2019.8983345.

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Sankar, Kannan, Rasna R. Walia, Carla M. Mann, Robert L. Jernigan, Vasant G. Honavar, and Drena Dobbs. "An analysis of conformational changes upon RNA-protein binding." In BCB '14: ACM-BCB '14. New York, NY, USA: ACM, 2014. http://dx.doi.org/10.1145/2649387.2660790.

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Lehman, Stacey L., Theresa Wechsler, Gaelyn C. Lyons, Lisa M. Jenkins, Kevin Camphausen, and Philip J. Tofilon. "Abstract 3741: Identification of RNA binding proteins influenced by ionizing radiation through RNA interactome capture." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-3741.

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Lehman, Stacey L., Theresa Wechsler, Gaelyn C. Lyons, Lisa M. Jenkins, Kevin Camphausen, and Philip J. Tofilon. "Abstract 3741: Identification of RNA binding proteins influenced by ionizing radiation through RNA interactome capture." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-3741.

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Majumder, Mrinmoyee, Nallasivam Palanisamy, Shuo Qie, Terry Day, Alan J. Diehl, and Viswanathan Palanisamy. "Abstract 2849: RNA-binding protein FXR1 negatively regulates senescence by destabilizing mRNA CDKN1A and stabilizing noncoding RNA telomerase RNA component." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-2849.

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Towfic, Fadi, David C. Gemperline, Cornelia Caragea, Feihong Wu, Drena Dobbs, and Vasant Honavar. "Structural characterization of RNA-binding sites of proteins: Preliminary results." In 2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops. IEEE, 2007. http://dx.doi.org/10.1109/bibmw.2007.4425401.

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Kim, Hyun Min, Mi Jin Jeon, Seo Young Park, Sang Hoon Ma, and Young Hee Joung. "Functional Characterization of RNA-Binding Protein Isolated from Hot Pepper." In The 3rd World Congress on New Technologies. Avestia Publishing, 2017. http://dx.doi.org/10.11159/icbb17.123.

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Reports on the topic "RNA-binding"

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Atasoy, Ulus, J. W. Davis, and Tim Hoffman. RNA Binding Proteins Posttranscriptionally Regulate Genes Involved In Oncogenesis. Fort Belvoir, VA: Defense Technical Information Center, June 2010. http://dx.doi.org/10.21236/ada540837.

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Brewer, Gary. RNA-Binding Proteins as Novel Oncoproteins and Tumor Suppressors in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, May 2004. http://dx.doi.org/10.21236/ada436941.

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Brewer, Gary. RNA-Binding Proteins as Novel Oncoproteins and Tumor Suppressors in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, May 2006. http://dx.doi.org/10.21236/ada456197.

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Brewer, Gary. RNA-Binding Proteins as Novel Oncogenes and Tumor Suppressors in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, May 2005. http://dx.doi.org/10.21236/ada474438.

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Gafni, Yedidya, and Vitaly Citovsky. Inactivation of SGS3 as Molecular Basis for RNA Silencing Suppression by TYLCV V2. United States Department of Agriculture, November 2013. http://dx.doi.org/10.32747/2013.7593402.bard.

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The Israeli isolate of Tomato yellow leaf curl geminivirus(TYLCV-Is) is a major tomato pathogen, causing extensive crop losses in Israel and in the south-eastern U.S. Yet, little is known about the molecular mechanisms of its interaction with tomato cells. One of the most interesting aspects of such interaction is how the invading virus counteracts the RNA silencing response of the plant. In the former BARD project, we have shown that TYLCV-Is V2 protein is an RNA silencing suppressor, and that this suppression is carried out via the interaction of V2 with the SGS3 component of the plant RNA silencing machinery. This reported project was meant to use our data as a foundation to elucidate the molecular mechanism by which V2 affects the SGS3 activity. While this research is likely to have an important impact on our understanding of basic biology of virus-plant interactions and suppression of plant immunity, it also will have practical implications, helping to conceive novel strategies for crop resistance to TYLCV-Is. Our preliminary data in regard to V2 activities and our present knowledge of the SGS3 function suggest likely mechanisms for the inhibitory effect of V2 on SGS3. We have shown that V2 possess structural and functional hallmarks of an F-box protein, suggesting that it may target SGS3 for proteasomal degradation. SGS3 contains an RNA-binding domain and likely functions to protect the cleavage produces of the primary transcript for subsequent conversion to double-stranded forms; thus, V2 may simply block the RNA binding activity of SGS3. V2 may also employ a combination of these mechanisms. These and other possibilities were tested in this reported project.

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Hale, Benjamin J., Caixia Yang, and Jason W. Ross. Expression of RNA Binding Proteins DND1 and FXR1 in the Porcine Uterus during the Estrous Cycle and Early Pregnancy. Ames (Iowa): Iowa State University, January 2013. http://dx.doi.org/10.31274/ans_air-180814-832.

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Whitham, Steven A., Amit Gal-On, and Victor Gaba. Post-transcriptional Regulation of Host Genes Involved with Symptom Expression in Potyviral Infections. United States Department of Agriculture, June 2012. http://dx.doi.org/10.32747/2012.7593391.bard.

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Understanding how RNA viruses cause disease symptoms in their hosts is expected to provide information that can be exploited to enhance modern agriculture. The helper component-proteinase (HC-Pro) protein of potyviruses has been implicated in symptom development. Previously, we demonstrated that symptom expression is associated with binding of duplex small-interfering-RNA (duplex-siRNA) to a highly conserved FRNK amino acid motif in the HC-Pro of Zucchini yellow mosaic virus (ZYMV). This binding activity also alters host microRNA (miRNA) profiles. In Turnip mosaic virus (TuMV), which infects the model plant Arabidopsis, mutation of the FRNK motif to FINK was lethal providing further indication of the importance of this motif to HC-Pro function. In this continuation project, our goal was to further investigate how ZYMV and TuMV cause the mis-expression of genes in cucurbits and Arabidopsis, respectively, and to correlate altered gene expression with disease symptoms. Objective 1 was to examine the roles of aromatic and positively charged residues F164RNH and K215RLF adjacent to FR180NK in small RNA binding. Objective 2 was to determine the target genes of the miRNAs which change during HC-Pro expression in infected tissues and transgenic cucumber. Objective 3 was to characterize RNA silencing mechanisms underlying differential expression of host genes. Objective 4 was to analyze the function of miRNA target genes and differentially expressed genes in potyvirus-infected tissues. We found that the charged K/R amino acid residues in the FKNH and KRLF motifs are essential for virus viability. Replacement of K to I in FKNH disrupted duplex-siRNA binding and virus infectivity, while in KRLF mutants duplex-siRNA binding was maintained and virus infectivity was limited: symptomless following a recovery phenomenon. These findings expanded the duplex-siRNA binding activity of HC-Pro to include the adjacent FRNK and FRNH sites. ZYMV causes many squash miRNAs to hyper-accumulate such as miR166, miR390, mir168, and many others. Screening of mir target genes showed that only INCURVATA-4 and PHAVOLUTA were significantly upregulated following ZYMVFRNK infection. Supporting this finding, we found similar developmental symptoms in transgenic Arabidopsis overexpressing P1-HC-Pro of a range of potyviruses to those observed in miR166 mutants. We characterized increased transcription of AGO1 in response to infection with both ZYMV strains. Differences in viral siRNA profiles and accumulation between mild and severe virus infections were characterized by Illumina sequencing, probably due to the differences in HC-Pro binding activity. We determined that the TuMV FINK mutant could accumulate and cause symptoms in dcl2 dcl4 or dcl2 dcl3 dcl4 mutants similar to TuMV FRNK in wild type Arabidopsis plants. These dcl mutant plants are defective in antiviral defenses, and the results show that factors other than HC-ProFRNK motif can induce symptoms in virus-infected plants. As a result of this work, we have a better understanding of the FRNK and FKNH amino acid motifs of HC-Pro and their contributions to the duplex-siRNA binding functions. We have identified plant genes that potentially contribute to infectivity and symptoms of virus infected plants when they are mis-expressed during potyviral infections. The results establish that there are multiple underlying molecular mechanisms that lead viral pathogenicity, some dependent on HC-Pro. The potential benefits include the development of novel strategies for controlling diseases caused by viruses, methods to ensure stable expression of transgenes in genetically improved crops, and improved potyvirus vectors for expression of proteins or peptides in plants.

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Liao, Jianhua, Jingting Liu, Baoqing Liu, Chunyan Meng, and Peiwen Yuan. Effect of OIP5-AS1 on clinicopathological characteristics and prognosis of cancer patients: a meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, October 2022. http://dx.doi.org/10.37766/inplasy2022.10.0118.

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Review question / Objective: According to recent studies, long non-coding RNA (lncRNAs) i.e., OPA-interacting protein 5 antisense RNA 1 (OIP5-AS1) has an important role in various carcinomas. However, its role in the cancer is contradictory. Therefore, we aimed to evaluate the link between OIP5-AS1 and cancer patients' clinicopathological characteristics and prognosis to better understand OIP5-AS1's role in cancer. Condition being studied: Reported studies have revealed that long non-coding RNA (lncRNAs) are considerably involved in crucial physiological events in several carcinomas, it can inhibit or promote the occurrence and development of tumors by changing the sequence and spatial structure, modulating epigenetic, regulating the expression level and interacting with binding proteins. However, the mechanism of cancer regulation via lncRNAs was incompletely understood. Hence, clarifying the application value of lncRNAs in preclinical and clinical disease diagnosis and treatment was therefore the prime objective in the field of cancer research at the time.

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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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Whitham, Steven A., Amit Gal-On, and Tzahi Arazi. Functional analysis of virus and host components that mediate potyvirus-induced diseases. United States Department of Agriculture, March 2008. http://dx.doi.org/10.32747/2008.7591732.bard.

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The mechanisms underlying the development of symptoms in response to virus infection remain to be discovered in plants. Insight into symptoms induced by potyviruses comes from evidence implicating the potyviral HC-Pro protein in symptom development. In particular, recent studies link the development of symptoms in infected plants to HC-Pro's ability to interfere with small RNA metabolism and function in plant hosts. Moreover, mutation of the highly conserved FRNK amino acid motif to FINK in the HC-Pro of Zucchini yellow mosaic virus (ZYMV) converts a severe strain into an asymptomatic strain, but does not affect virus accumulation in cucurbit hosts. The ability of this FINK mutation to uncouple symptoms from virus accumulation creates a unique opportunity to study symptom etiology, which is usually confounded by simultaneous attenuation of both symptoms and virus accumulation. Our goal was to determine how mutations in the conserved FRNK motif affect host responses to potyvirus infection in cucurbits and Arabidopsis thaliana. Our first objective was to define those amino acids in the FRNK motif that are required for symptoms by mutating the FRNK motif in ZYMV and Turnip mosaic virus (TuMV). Symptom expression and accumulation of resulting mutant viruses in cucurbits and Arabidopsis was determined. Our second objective was to identify plant genes associated with virus disease symptoms by profiling gene expression in cucurbits and Arabidopsis in response to mutant and wild type ZYMV and TuMV, respectively. Genes from the two host species that are differentially expressed led us to focus on a subset of genes that are expected to be involved in symptom expression. Our third objective was to determine the functions of small RNA species in response to mutant and wild type HC-Pro protein expression by monitoring the accumulation of small RNAs and their targets in Arabidopsis and cucurbit plants infected with wild type and mutant TuMV and ZYMV, respectively. We have found that the maintenance of the charge of the amino acids in the FRNK motif of HC-Pro is required for symptom expression. Reduced charge (FRNA, FRNL) lessen virus symptoms, and maintain the suppression of RNA silencing. The FRNK motif is involved in binding of small RNA species including microRNAs (miRNA) and short interfering RNAs (siRNA). This binding activity mediated by the FRNK motif has a role in protecting the viral genome from degradation by the host RNA silencing system. However, it also provides a mechanism by which the FRNK motif participates in inducing the symptoms of viral infection. Small RNA species, such as miRNA and siRNA, can regulate the functions of plant genes that affect plant growth and development. Thus, this binding activity suggests a mechanism by which ZYMVHC-Pro can interfere with plant development resulting in disease symptoms. Because the host genes regulated by small RNAs are known, we have identified candidate host genes that are expected to play a role in symptoms when their regulation is disrupted during viral infections. As a result of this work, we have a better understanding of the FRNK amino acid motif of HC-Pro and its contribution to the functions of HC-Pro, and we have identified plant genes that potentially contribute to symptoms of virus infected plants when their expression becomes misregulated during potyviral infections. The results set the stage to establish the roles of specific host genes in viral pathogenicity. The potential benefits include the development of novel strategies for controlling diseases caused by viruses, methods to ensure stable expression of transgenes in genetically improved crops, and improved potyvirus vectors for expression of proteins or peptides in plants.

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