Relevant bibliographies by topics / RNA-protein interactions

Contents

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

Academic literature on the topic 'RNA-protein interactions'

Author: Grafiati
Published: 4 June 2021
Last updated: 6 September 2023

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Journal articles on the topic "RNA-protein interactions"

1

Hall, Kathleen B. "RNA–protein interactions." Current Opinion in Structural Biology 12, no. 3 (June 2002): 283–88. http://dx.doi.org/10.1016/s0959-440x(02)00323-8.

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Wickens, Marvin P., and James E. Dahlberg. "RNA-protein interactions." Cell 51, no. 3 (November 1987): 339–42. http://dx.doi.org/10.1016/0092-8674(87)90629-5.

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Frankel, Alan D., Iain W. Mattaj, and Donald C. Rio. "RNA-protein interactions." Cell 67, no. 6 (December 1991): 1041–46. http://dx.doi.org/10.1016/0092-8674(91)90282-4.

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Nagai, Kiyoshi. "RNA-protein interactions." Current Opinion in Structural Biology 2, no. 1 (February 1992): 131–37. http://dx.doi.org/10.1016/0959-440x(92)90188-d.

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Puglisi, Joseph D. "RNA-protein interactions." Chemistry & Biology 2, no. 9 (September 1995): 581. http://dx.doi.org/10.1016/1074-5521(95)90121-3.

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Struhl, Kevin. "RNA-Protein Interactions." Current Protocols in Molecular Biology 73, no. 1 (January 2006): 27.0.1. http://dx.doi.org/10.1002/0471142727.mb2700s73.

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Garrett, Roger A. "RNA-protein interactions." FEBS Letters 375, no. 3 (November 20, 1995): 313. http://dx.doi.org/10.1016/0014-5793(95)90104-3.

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Doetsch, Martina, Renée Schroeder, and Boris Fürtig. "Transient RNA-protein interactions in RNA folding." FEBS Journal 278, no. 10 (April 13, 2011): 1634–42. http://dx.doi.org/10.1111/j.1742-4658.2011.08094.x.

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Osório, Joana. "Exploring protein–RNA interactions with RNA Tagging." Nature Reviews Genetics 17, no. 1 (November 16, 2015): 7. http://dx.doi.org/10.1038/nrg.2015.6.

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Predki, Paul F., L. Mike Nayak, Morris B. C. Gottlieb, and Lynne Regan. "Dissecting RNA-protein interactions: RNA-RNA recognition by Rop." Cell 80, no. 1 (January 1995): 41–50. http://dx.doi.org/10.1016/0092-8674(95)90449-2.

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Dissertations / Theses on the topic "RNA-protein interactions"

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Hahn, Daniela. "Brr2 RNA helicase and its protein and RNA interactions." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5775.

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The dynamic rearrangements of RNA and protein complexes and the fidelity of pre-mRNA splicing are governed by DExD/H-box ATPases. One of the spliceosomal ATPases, Brr2, is believed to facilitate conformational rearrangements during spliceosome activation and disassembly. It features an unusual architecture, with two consecutive helicase-cassettes, each comprising a helicase and a Sec63 domain. Only the N-terminal cassette exhibits catalytic activity. By contrast, the C-terminal half of Brr2 engages in protein interactions. Amongst interacting proteins are the Prp2 and Prp16 helicases. The work presented in this thesis aimed at studying and assigning functional relevance to the bipartite architecture of Brr2 and addressed the following questions: (1) What role does the catalytically inert C-terminal half play in Brr2 function, and why does it interact with other RNA helicases? (2) Which RNAs interact with the different parts of Brr2? (1) In a yeast two-hybrid screen novel brr2 mutant alleles were identified by virtue of abnormal protein interactions with Prp2 and Prp16. Phenotypic characterization showed that brr2 C-terminus mutants exhibit a splicing defect, demonstrating that an intact C-terminus is required for Brr2 function. ATPase/helicase deficient prp16 mutants suppress the interaction defect of brr2 alleles, possibly indicating an involvement of the Brr2 C-terminus in the regulation of interacting helicases. (2) Brr2-RNA interactions were identified by the CRAC approach (in vivo Crosslinking and analysis of cDNA). Physical separation of the N-terminal and C-terminal portions and their individual analyses indicate that only the N-terminus of Brr2 interacts with RNA. Brr2 cross-links in the U4 and U6 snRNAs suggest a step-wise dissociation of the U4/U6 duplex during catalytic activation of the spliceosome. Newly identified Brr2 cross-links in the U5 snRNA and in pre-mRNAs close to 3’ splice sites are supported by genetic analyses. A reduction of second step efficiency upon combining brr2 and U5 mutations suggests an involvement of Brr2 in the second step of splicing. An approach now described as CLASH (Cross-linking, Ligation and Sequencing of Hybrids) identified Brr2 associated chimeric sequencing reads. The inspection of chimeric U2-U2 sequences suggests a revised secondary structure for the U2 snRNA, which was confirmed by phylogenentic and mutational analyses. Taken together these findings underscore the functional distinction of the N- and C-terminal portions of Brr2 and add mechanistic relevance to its bipartite architecture. The catalytically active N-terminal helicase-cassette is required to establish RNA interactions and to provide helicase activity. Conversely, the C-terminal helicase-cassette functions solely as protein interaction domain, possibly exerting regulation on the activities of interacting helicases and Brr2 itself.
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Chandran, V. "Structural and functional characterisation of the protein-protein and protein-RNA interactions in the RNA degradosome." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.597437.

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The C-terminal domain of RNase E is intrinsically unstructured, but small segments of 13 to 80 residues are predicted to have propensity for defined conformation and evidence presented here indicates that they function in nucleic acid binding and protein-protein interactions in the degradosome. Binding of two of these ordered regions to their predicted partners, enolase and PNPase, has been demonstrated using non-dissociating nano-flow mass spectrometry (MS). Binding of helicase to an arginine rich domain of RNase E (residues 628-843) has also been shown by MS and other approaches. The binding stoichiometry for the various degradosome components with minimal binding regions on RNase E is also provided by non-dissociating MS, and these data provide insight into the organisation of the degradosome. The crystal structure of E. coli enolase in complex with a synthetic peptide corresponding to the proposed recognition in the degradosome (RNase E residues 833-850) has been solved to 1.6Å resolution. The crystal structure reveals a 1:1 complex of the peptide with the enolase dimer. It is predicted that enolase and RNase E interact specifically and stably in many Gram-negative pathogens, with implications for a common mode of regulated turnover of targeted transcripts. An analysis of the metabolome data from wild type E. coli cells and the degradosome mutant strains grown normally and under phosphosugar stress signify the importance of coordinated RNA degradation by the organisation of a degradosome machinery in regulating cellular responses to physiological stress stimuli.
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Batal, Rami. "RNA and protein interactions of the measles virus nucleocapsid protein." Thesis, McGill University, 1994. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=55437.

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We are interested in studying the RNA and protein binding activities of the measles virus (MV) NP. MV is one of the members of Paramyxoviridae, a family of non-segmented negative-stranded RNA viruses family. We have expressed the MV NP in procaryotic systems and by in vitro translation. We have created a number of carboxy-terminal deletions of NP to use in mapping the domains involved in RNA and protein binding. We have transcribed the 5$ sp prime$ end antigenome sequences (positive leader) in vitro. We have metabolically labeled viral and MV-infected cellular proteins. We have applied different RNA-protein and protein-protein binding assays in order to study the postulated binding. We were not able to unequivocally detect specific binding between NP and the RNA. However, we have observed significant binding between NP and each of three MV-specific proteins NP, P, and M. Furthermore, we have found that the carboxy terminus of NP is important in this binding. Deletions in that domain will abolish M binding, and further deletions towards the amino terminus will abolish P binding, and eventually NP binding. Successively larger carboxy-terminal deletions first abolish NP binding to M, then to P, and then eventually to itself.
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Xu, Deming. "RNA and protein interactions in the yeast spliceosome." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape10/PQDD_0005/NQ41534.pdf.

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Turner, David Richard. "Protein-RNA interactions in tobacco mosaic virus assembly." Thesis, University of Cambridge, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328799.

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Singh, Jagjit. "RNA-Protein Interactions in the U12-Dependent Spliceosome." Cleveland State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=csu1484307043050366.

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Terribilini, Michael Joseph. "Computational analysis and prediction of protein-RNA interactions." [Ames, Iowa : Iowa State University], 2008.

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Peters, Daniel. "Structural and biochemical investigation of protein-RNA interactions." Thesis, University of York, 2014. http://etheses.whiterose.ac.uk/6784/.

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Non-coding RNAs (ncRNAs) are nucleic acids that do not code for protein. Rather, they have evolved highly specialised secondary structures and catalytic mechanisms that place them at the heart of regulating gene expression. The function of ncRNAs is often mediated or dependent on their interactions with RNA binding proteins. The study of both the structure and function of these proteins is crucial for understanding the biological role of the protein-RNA complexes. In this thesis, the structure and function of two RNA binding proteins: Lin28 and dihydrouridine synthase C (DusC) were investigated using X-ray crystallography and biophysical techniques. In both systems, the specific recognition of target molecules is important for function. The aim of the study was therefore to use structural and functional data to elucidate the molecular basis of these protein-RNA interactions. There are three main findings: (1) specific recognition of microRNAs by Lin28 is dependent on the interaction of the Zinc Knuckle domain of the protein with a 3’ GGAG motif; (2) non-specific, electrostatic interactions between the cold-shock domain of Lin28 and RNA suggest a transcriptome scanning mechanism for recognising Lin28 targets; and (3) modification of specific nucleotide positions within tRNA by DusC is dependent on the orientation in which the tRNA is bound, which is determined by minor changes in the protein structure. These findings have helped to elucidate the mechanisms, and hence biological functions, of these RNA binding proteins. Both proteins have been previously associated with cancer. Through greater understanding of the molecular basis of these protein-RNA interactions, the production of novel therapeutic agents can be informed, which can help to combat disease. This data will therefore aid future efforts to treat and prevent the cancers caused by the aberrant actions of these RNA binding proteins.
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Ellis, Jonathan James. "Towards the prediction of protein-RNA interactions through protein structure analysis." Thesis, University of Sussex, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.444117.

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Ribeiro, Diogo. "Discovery of the role of protein-RNA interactions in protein multifunctionality and cellular complexity." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0449/document.

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Au fil du temps, la vie a évolué pour produire des organismes remarquablement complexes. Pour faire face à cette complexité, les organismes ont développé une pléthore de mécanismes régulateurs. Par exemple, les mammifères transcrivent des milliers d'ARN longs non codants (ARNlnc), accroissant ainsi la capacité régulatrice de leurs cellules. Un concept émergent est que les ARNlnc peuvent servir d'échafaudages aux complexes protéiques, mais la prévalence de ce mécanisme n'a pas encore été démontrée. De plus, pour chaque ARN messager, plusieurs régions 3’ non traduites (3’UTRs) sont souvent présentes. Ces 3’UTRs pourraient réguler la fonction de la protéine en cours de traduction, en participant à la formation des complexes protéiques dans lesquels elle est impliquée. Néanmoins, la fréquence et l’importance ce mécanisme reste à aborder.Cette thèse a pour objectif de découvrir et comprendre systématiquement ces deux mécanismes de régulation méconnus. Concrètement, l'assemblage de complexes protéiques promus par les ARNlnc et les 3'UTRs est étudié avec des données d’interactions protéines-protéines et protéines-ARN à grande échelle. Ceci a permis (i) de prédire le rôle de plusieurs centaines d'ARNlnc comme molécules d'échafaudage pour plus de la moitié des complexes protéiques connus, ainsi que (ii) d’inférer plus d’un millier de complexes 3'UTR-protéines, dont certains cas pourraient réguler post-traductionnellement des protéines moonlighting aux fonctions multiples et distinctes. Ces résultats indiquent qu'une proportion élevée d'ARNlnc et de 3'UTRs pourrait réguler la fonction des protéines en augmentant ainsi la complexité du vivant
Over time, life has evolved to produce remarkably complex organisms. To cope with this complexity, organisms have evolved a plethora of regulatory mechanisms. For instance, thousands of long non-coding RNAs (lncRNAs) are transcribed by mammalian genomes, presumably expanding their regulatory capacity. An emerging concept is that lncRNAs can serve as protein scaffolds, bringing proteins in proximity, but the prevalence of this mechanism is yet to be demonstrated. In addition, for every messenger RNA encoding a protein, regulatory 3’ untranslated regions (3’UTRs) are also present. Recently, 3’UTRs were shown to form protein complexes during translation, affecting the function of the protein under synthesis. However, the extent and importance of these 3’UTR-protein complexes in cells remains to be assessed.This thesis aims to systematically discover and provide insights into two ill-known regulatory mechanisms involving the non-coding portion of the human transcriptome. Concretely, the assembly of protein complexes promoted by lncRNAs and 3’UTRs is investigated using large-scale datasets of protein-protein and protein-RNA interactions. This enabled to (i) predict hundreds of lncRNAs as possible scaffolding molecules for more than half of the known protein complexes, as well as (ii) infer more than a thousand distinct 3’UTR-protein complexes, including cases likely to post-translationally regulate moonlighting proteins, proteins that perform multiple unrelated functions. These results indicate that a high proportion of lncRNAs and 3’UTRs may be employed in regulating protein function, potentially playing a role both as regulators and as components of complexity
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Books on the topic "RNA-protein interactions"

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Kiyoshi, Nagai, and Mattaj Iain W, eds. RNA-protein interactions. Oxford: IRL Press at Oxford University Press, 1994.

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Lin, Ren-Jang, ed. RNA-Protein Complexes and Interactions. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3591-8.

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Joo, Chirlmin, and David Rueda, eds. Biophysics of RNA-Protein Interactions. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9726-8.

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Lin, Ren-Jang, ed. RNA-Protein Complexes and Interactions. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3191-1.

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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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J, Smith Christopher W., ed. RNA-protein interactions: A practical approach. Oxford: Oxford University Press, 1998.

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A, Rice Phoebe, and Correll Carl C, eds. Protein-nucleic acid interactions: Structural biology. Cambridge: RSC Pub., 2008.

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Koloteva, Nadejda. Regulation of eukaryotic gene expression via RNA-RNA and RNA-protein interactions. Manchester: UMIST, 1997.

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Munschauer, Mathias. High-Resolution Profiling of Protein-RNA Interactions. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-16253-9.

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Book chapters on the topic "RNA-protein interactions"

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Manoharan, Vijayalaxmi, Jose Manuel Pérez-Cañadillas, and Andres Ramos. "Protein-RNA Interactions." In NMR of Biomolecules, 218–36. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527644506.ch12.

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Turnbull, Andrew P., and Xiaoqiu Wu. "Studying RNA–Protein Complexes Using." In Protein-Ligand Interactions, 423–46. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5_20.

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Martin, Stephen R., Andres Ramos, and Laura Masino. "Biolayer Interferometry: Protein–RNA Interactions." In Protein-Ligand Interactions, 351–68. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5_16.

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Lamichhane, Rajan. "How Proteins Recognize RNA." In Biophysics of RNA-Protein Interactions, 3–21. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9726-8_1.

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Sprinzl, M., H. P. Hoffmann, S. Brock, M. Nanninga, and V. Hornung. "RNA-Aptamers for Studying RNA Protein Interactions." In RNA Biochemistry and Biotechnology, 217–28. Dordrecht: Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4485-8_16.

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Lang, Matti A., and Françoise Raffalli-Mathieu. "Cytochrome P450 RNA—Protein Interactions." In Endocrine Updates, 225–38. Boston, MA: Springer US, 2002. http://dx.doi.org/10.1007/978-1-4757-6446-8_13.

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Kumarevel, Thirumananseri. "Barium and Protein–RNA Interactions." In Encyclopedia of Metalloproteins, 223–36. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-1533-6_169.

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Re, Angela, Tejal Joshi, Eleonora Kulberkyte, Quaid Morris, and Christopher T. Workman. "RNA–Protein Interactions: An Overview." In Methods in Molecular Biology, 491–521. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-709-9_23.

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Fareh, Mohamed. "Dynamics of MicroRNA Biogenesis." In Biophysics of RNA-Protein Interactions, 211–49. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9726-8_10.

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Huang, Lin, and David M. J. Lilley. "The Interaction Between L7Ae Family of Proteins and RNA Kink Turns." In Biophysics of RNA-Protein Interactions, 23–37. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9726-8_2.

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Conference papers on the topic "RNA-protein interactions"

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Orenstein, Yaron. "Computational Modeling of Protein-RNA Interactions." In BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3107411.3107495.

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Wang, Tong, Hongmei Li, Xiaoming Hu, and Xiaoxia Cao. "Predicting RNA-protein interactions using a novel method." In 2012 5th International Conference on Biomedical Engineering and Informatics (BMEI). IEEE, 2012. http://dx.doi.org/10.1109/bmei.2012.6513097.

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Tong Wang, Zhizhen Yang, Wenan Tan, and Xiaoming Hu. "Identifying RNA-protein interactions using feature dimension reduction method." In 2013 8th International Conference on Computer Science & Education (ICCSE). IEEE, 2013. http://dx.doi.org/10.1109/iccse.2013.6554053.

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BLENCOWE, BENJAMIN, STEVEN BRENNER, TIMOTHY HUGHES, and QUAID MORRIS. "POST-TRANSCRIPTIONAL GENE REGULATION: RNA-PROTEIN INTERACTIONS, RNA PROCESSING, MRNA STABILITY AND LOCALIZATION." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2008. http://dx.doi.org/10.1142/9789812836939_0052.

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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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Eikje, Natalja Skrebova. "DNA-RNA, DNA-DNA, DNA-protein and protein-protein interactions in diagnosis of skin cancers by FT-IR microspectroscopy." In SPIE BiOS. SPIE, 2011. http://dx.doi.org/10.1117/12.874692.

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Shaw, Harry, Nagarajan Pattabiraman, Deborah Preston, Tatiana Ammosova, Yuri Obukhov, Sergei Nekhai, and Ajit Kumar. "Information theory and signal processing methodology to identify nucleic acid-protein binding sequences in RNA-protein interactions." In 2019 53rd Annual Conference on Information Sciences and Systems (CISS). IEEE, 2019. http://dx.doi.org/10.1109/ciss.2019.8692826.

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Zhang, Kaiming, Yiqun Xiao, Xiaoyong Pan, and Yang Yang. "Prediction of RNA-protein interactions with distributed feature representations and a hybrid deep model." In ICIMCS'18: The 10th International Conference on Internet Multimedia Computing and Service. New York, NY, USA: ACM, 2018. http://dx.doi.org/10.1145/3240876.3240912.

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San, Avdar, Anjana Saxena, and Shaneen Singh. "Abstract 844: RNA binding domains of nucleolin exhibit specificity in driving nucleolin-miRNA interactions: Anin silicomodeling and RNA-protein docking study." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-844.

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Northwood, K., J. Saunus, M. Milevskiy, S. Lakhani, and M. Brown. "Abstract P1-04-05: RNA immunoprecipitation reveals lncRNA-protein interactions in basal-like breast cancer." In Abstracts: 2016 San Antonio Breast Cancer Symposium; December 6-10, 2016; San Antonio, Texas. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.sabcs16-p1-04-05.

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Reports on the topic "RNA-protein interactions"

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Lee, Jae-Hyung. Analysis of Protein-RNA and Protein-Peptide Interactions in Equine Infectious Anemia. Office of Scientific and Technical Information (OSTI), January 2007. http://dx.doi.org/10.2172/933138.

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Citovsky, Vitaly, and Yedidya Gafni. Suppression of RNA Silencing by TYLCV During Viral Infection. United States Department of Agriculture, December 2009. http://dx.doi.org/10.32747/2009.7592126.bard.

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The Israeli isolate of Tomato yellow leaf curl geminivirus (TYLCV-Is) is a major tomato pathogen, causing extensive (up to 100%) crop losses in Israel and in the south-eastern U.S. (e.g., Georgia, Florida). Surprisingly, however, little is known about the molecular mechanisms of TYLCV-Is interactions with tomato cells. In the current BARD project, we have identified a TYLCV-Is protein, V2, which acts as a suppressor of RNA silencing, and showed that V2 interacts with the tomato (L. esculentum) member of the SGS3 (LeSGS3) protein family known to be involved in RNA silencing. This proposal will use our data as a foundation to study one of the most intriguing, yet poorly understood, aspects of TYLCV-Is interactions with its host plants – possible involvement of the host innate immune system, i.e., RNA silencing, in plant defense against TYLCV-Is and the molecular pathway(s) by which TYLCV-Is may counter this defense. Our project sought two objectives: I. Study of the roles of RNA silencing and its suppression by V2 in TYLCV-Is infection of tomato plants. II. Study of the mechanism by which V2 suppresses RNA silencing. Our research towards these goals has produced the following main achievements: • Identification and characterization of TYLCV V2 protein as a suppressor of RNA silencing. (#1 in the list of publications). • Characterization of the V2 protein as a cytoplasmic protein interacting with the plant protein SlSGS3 and localized mainly in specific, not yet identified, bodies. (#2 in the list of publications). • Development of new tools to study subcellular localization of interacting proteins (#3 in the list of publications). • Characterization of TYLCV V2 as a F-BOX protein and its possible role in target protein(s) degradation. • Characterization of TYLCV V2 interaction with a tomato cystein protease that acts as an anti-viral agent. These research findings provided significant insights into (I) the suppression of RNA silencing executed by the TYLCV V2 protein and (II) characterization some parts of the mechanism(s) involved in this suppression. The obtained knowledge will help to develop specific strategies to attenuate TYLCV infection, for example, by blocking the activity of the viral suppressor of gene silencing thus enabling the host cell silencing machinery combat the virus.
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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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Gafni, Yedidya, Moshe Lapidot, and Vitaly Citovsky. Dual role of the TYLCV protein V2 in suppressing the host plant defense. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7597935.bard.

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TYLCV-Is is a major tomato pathogen, causing extensive crop losses in Israel and the U.S. We have identified a TYLCV-Is protein, V2, which acts as a suppressor of RNA silencing. Intriguingly, the counter-defense function of V2 may not be limited to silencing suppression. Our recent data suggest that V2 interacts with the tomato CYP1 protease. CYP1 belongs to the family of papain-like cysteine proteases which participate in programmed cell death (PCD) involved in plant defense against pathogens. Based on these data we proposed a model for dual action of V2 in suppressing the host antiviral defense: V2 targets SGS3 for degradation and V2 inhibits CYP1 activity. To study this we proposed to tackle three specific objectives. I. Characterize the role of V2 in SGS3 proteasomal degradation ubiquitination, II. Study the effects of V2 on CYP1 maturation, enzymatic activity, and accumulation and, III. Analyze the effects of the CYP1-V2 interaction on TYLCV-Is infection. Here we describe results from our study that support our hypothesis: the involvement of the host's innate immune system—in this case, PCD—in plant defense against TYLCV-Is. Also, we use TYLCV-Is to discover the molecular pathway(s) by which this plant virus counters this defense. Towards the end of our study we discovered an interesting involvement of the C2 protein encoded by TYLCV-Is in inducing Hypersensitive Response in N. benthamianaplants which is not the case when the whole viral genome is introduced. This might lead to a better understanding of the multiple processes involved in the way TYLCV is overcoming the defense mechanisms of the host plant cell. In a parallel research supporting the main goal described, we also investigated Agrobacteriumtumefaciens-encoded F-box protein VirF. It has been proposed that VirF targets a host protein for the UPS-mediated degradation, very much the way TYLCV V2 does. In our study, we identified one such interactor, an Arabidopsistrihelix-domain transcription factor VFP3, and further show that its very close homolog VFP5 also interacted with VirF. Interestingly, interactions of VirF with either VFP3 or VFP5 did not activate the host UPS, suggesting that VirF might play other UPS-independent roles in bacterial infection. Another target for VirF is VFP4, a transcription factor that both VirF and its plant functional homolog VBF target to degradation by UPS. Using RNA-seqtranscriptome analysis we showed that VFP4 regulates numerous plant genes involved in disease response, including responses to viral and bacterial infections. Detailed analyses of some of these genes indicated their involvement in plant protection against Agrobacterium infection. Thus, Agrobacterium may facilitate its infection by utilizing the host cell UPS to destabilize transcriptional regulators of the host disease response machinery that limits the infection.
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Stern, David, and Gadi Schuster. Manipulation of Gene Expression in the Chloroplast. United States Department of Agriculture, September 2000. http://dx.doi.org/10.32747/2000.7575289.bard.

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The steady-state level of a given mRNA is determined by its rates of transcription and degradation. The stabilities of chloroplast mRNAs vary during plant development, in part regulating gene expression. Furthermore, the fitness of the organelle depends on its ability to destroy non-functional transcripts. In addition, there is a resurgent interest by the biotechnology community in chloroplast transformation due to the public concerns over pollen transmission of introduced traits or foreign proteins. Therefore, studies into basic gene expression mechanisms in the chloroplast will open the door to take advantage of these opportunities. This project was aimed at gaining mechanistic insights into mRNA processing and degradation in the chloroplast and to engineer transcripts of varying stability in Chlamydomonas reinhardtii cells. This research uncovered new and important information on chloroplast mRNA stability, processing, degradation and translation. In particular, the processing of the 3' untranslated regions of chloroplast mRNAs was shown to be important determinants in translation. The endonucleolytic site in the 3' untranslated region was characterized by site directed mutagensis. RNA polyadenylation has been characterized in the chloroplast of Chlamydomonas reinhardtii and chloroplast transformants carrying polyadenylated sequences were constructed and analyzed. Data obtained to date suggest that chloroplasts have gene regulatory mechanisms which are uniquely adapted to their post-endosymbiotic environment, including those that regulate RNA stability. An exciting point has been reached, because molecular genetic studies have defined critical RNA-protein interactions that participate in these processes. However, much remains to be learned about these multiple pathways, how they interact with each other, and how many nuclear genes are consecrated to overseeing them. Chlamydomonas is an ideal model system to extend our understanding of these areas, given its ease of manipulation and the existing knowledge base, some of which we have generated.
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Rodriguez Muxica, Natalia. Open configuration options Bioinformatics for Researchers in Life Sciences: Tools and Learning Resources. Inter-American Development Bank, February 2022. http://dx.doi.org/10.18235/0003982.

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The COVID-19 pandemic has shown that bioinformatics--a multidisciplinary field that combines biological knowledge with computer programming concerned with the acquisition, storage, analysis, and dissemination of biological data--has a fundamental role in scientific research strategies in all disciplines involved in fighting the virus and its variants. It aids in sequencing and annotating genomes and their observed mutations; analyzing gene and protein expression; simulation and modeling of DNA, RNA, proteins and biomolecular interactions; and mining of biological literature, among many other critical areas of research. Studies suggest that bioinformatics skills in the Latin American and Caribbean region are relatively incipient, and thus its scientific systems cannot take full advantage of the increasing availability of bioinformatic tools and data. This dataset is a catalog of bioinformatics software for researchers and professionals working in life sciences. It includes more than 300 different tools for varied uses, such as data analysis, visualization, repositories and databases, data storage services, scientific communication, marketplace and collaboration, and lab resource management. Most tools are available as web-based or desktop applications, while others are programming libraries. It also includes 10 suggested entries for other third-party repositories that could be of use.
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Dickman, Martin B., and Oded Yarden. Genetic and chemical intervention in ROS signaling pathways affecting development and pathogenicity of Sclerotinia sclerotiorum. United States Department of Agriculture, July 2015. http://dx.doi.org/10.32747/2015.7699866.bard.

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Abstract: The long-term goals of our research are to understand the regulation of sclerotial development and pathogenicity in S. sclerotior11111. The focus in this project was on the elucidation of the signaling events and environmental cues involved in the regulation of these processes, utilizing and continuously developing tools our research groups have established and/or adapted for analysis of S. sclerotiorum, Our stated objectives: To take advantage of the recent conceptual (ROS/PPs signaling) and technical (amenability of S. sclerotiorumto manipulations coupled with chemical genomics and next generation sequencing) developments to address and extend our fundamental and potentially applicable knowledge of the following questions concerning the involvement of REDOX signaling and protein dephosphorylation in the regulation of hyphal/sclerotial development and pathogenicity of S. sclerotiorum: (i) How do defects in genes involved in ROS signaling affect S. sclerotiorumdevelopment and pathogenicity? (ii) In what manner do phosphotyrosinephosphatases affect S. sclerotiorumdevelopment and pathogenicity and how are they linked with ROS and other signaling pathways? And (iii) What is the nature of activity of newly identified compounds that affect S. sclerotiori,111 growth? What are the fungal targets and do they interfere with ROS signaling? We have met a significant portion of the specific goals set in our research project. Much of our work has been published. Briefly. we can summarize that: (a) Silencing of SsNox1(NADPHoxidase) expression indicated a central role for this enzyme in both virulence and pathogenic development, while inactivation of the SsNox2 gene resulted in limited sclerotial development, but the organism remained fully pathogenic. (b) A catalase gene (Scatl), whose expression was highly induced during host infection is involved in hyphal growth, branching, sclerotia formation and infection. (c) Protein tyrosine phosphatase l (ptpl) is required for sclerotial development and is involved in fungal infection. (d) Deletion of a superoxidedismutase gene (Sssodl) significantly reduced in virulence on both tomato and tobacco plants yet pathogenicity was mostly restored following supplementation with oxalate. (e) We have participated in comparative genome sequence analysis of S. sclerotiorumand B. cinerea. (f) S. sclerotiorumexhibits a potential switch between biotrophic and necrotrophic lifestyles (g) During plant­ microbe interactions cell death can occur in both resistant and susceptible events. Non­ pathogenic fungal mutants S. sclerotior111n also cause a cell death but with opposing results. We investigated PCD in more detail and showed that, although PCD occurs in both circumstances they exhibit distinctly different features. The mutants trigger a restricted cell death phenotype in the host that unexpectedly exhibits markers associated with the plant hypersensitive (resistant) response. Using electron and fluorescence microscopy, chemical effectors and reverse genetics, we have established that this restricted cell death is autophagic. Inhibition of autophagy rescued the non-pathogenic mutant phenotype. These findings indicate that autophagy is a defense response in this interaction Thus the control of cell death, dictated by the plant (autophagy) סr the fungus (apoptosis), is decisive to the outcome of certain plant­ microbe interactions. In addition to the time and efforts invested towards reaching the specific goals mentioned, both Pls have initiated utilizing (as stated as an objective in our proposal) state of the art RNA-seq tools in order to harness this technology for the study of S. sclerotiorum. The Pls have met twice (in Israel and in the US), in order to discuss .נחd coordinate the research efforts. This included a working visit at the US Pls laboratory for performing RNA-seq experiments and data analysis as well as working on a joint publication (now published). The work we have performed expands our understanding of the fundamental biology (developmental and pathogenic) of S. sclerotioז111וז. Furthermore, based on our results we have now reached the conclusion that this fungus is not a bona fide necrotroph, but can also display a biotrophic lifestyle at the early phases of infection. The data obtained can eventually serve .נ basis of rational intervention with the disease cycle of this pathogen.
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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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Elroy-Stein, Orna, and Dmitry Belostotsky. Mechanism of Internal Initiation of Translation in Plants. United States Department of Agriculture, December 2010. http://dx.doi.org/10.32747/2010.7696518.bard.

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Original objectives Elucidation of PABP's role in crTMV148 IRES function in-vitro using wheat germ extract and krebs-2 cells extract. Fully achieved. Elucidation of PABP's role in crTMV148 IRES function in-vivo in Arabidopsis. Characterization of the physical interactions of PABP and other potential ITAFs with crTMV148 IRES. Partly achieved. To conduct search for additional ITAFs using different approaches and evaluate the candidates. Partly achieved. Background of the topic The power of internal translation via the activity of internal ribosomal entry site (IRES) elements allow coordinated synthesis of multiple gene products from a single transcription unit, and thereby enables to bypass the need for sequential transformation with multiple independent transgenes. The key goal of this project was to identify and analyze the IRES-trans-acting factors (ITAFs) that mediate the activity of a crucifer-infecting tobamovirus (crTMV148) IRES. The remarkable conservation of the IRES activity across the phylogenetic spectrum (yeast, plants and animals) strongly suggests that key ITAFs that mediate its activity are themselves highly conserved. Thus, crTMV148 IRES offers opportunity for elucidation of the fundamental mechanisms underlying internal translation in higher plants in order to enable its rational manipulation for the purpose of agricultural biotechnology. Major conclusions and achievements. - CrTMV IRES requires PABP for maximal activity. This conclusion was achieved by PABP depletion and reconstitution of wheat germ- and Krebs2-derived in-vitro translation assays using Arabidopsis-derived PABP2, 3, 5, 8 and yeast Pab1p. - Mutations in the internal polypurine tract of the IRES decrease the high-affinity binding of all phylogenetically divergent PABPs derived from Arabidopsis and yeast in electro mobility gel shift assays. - Mutations in the internal polypurine tract decrease IRES activity in-vivo. - The 3'-poly(A) tail enhances crTMV148 IRES activity more efficiently in the absence of 5'-methylated cap. - In-vivo assembled RNPs containing proteins specifically associated with the IRES were purified from HEK293 cells using the RNA Affinity in Tandem (RAT) approach followed by their identification by mass spectroscopy. - This study yielded a list of potential protein candidates that may serve as ITAFs of crTMV148 IRES activity, among them are a/b tubulin, a/g actin, GAPDH, enolase 1, ribonuclease/angiogenin inhibitor 1, 26S proteasome subunit p45, rpSA, eEF1Bδ, and proteasome b5 subunit. Implications, both scientific and agriculture. The fact that the 3'-poly(A) tail enhances crTMV148 IRES activity more efficiently in the absence of 5'-methylated cap suggests a potential joint interaction between PABP, the IRES sequence and the 3'-poly(A). This has an important scientific implication related to IRES function in general.
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Savaldi-Goldstein, Sigal, and Todd C. Mockler. Precise Mapping of Growth Hormone Effects by Cell-Specific Gene Activation Response. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7699849.bard.

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Plant yield largely depends on a complex interplay and feedback mechanisms of distinct hormonal pathways. Over the past decade great progress has been made in elucidating the global molecular mechanisms by which each hormone is produced and perceived. However, our knowledge of how interactions between hormonal pathways are spatially and temporally regulated remains rudimentary. For example, we have demonstrated that although the BR receptor BRI1 is widely expressed, the perception of BRs in epidermal cells is sufficient to control whole-organ growth. Supported by additional recent works, it is apparent that hormones are acting in selected cells of the plant body to regulate organ growth, and furthermore, that local cell-cell communication is an important mechanism. In this proposal our goals were to identify the global profile of translated genes in response to BR stimulation and depletion in specific tissues in Arabidopsis; determine the spatio-temporal dependency of BR response on auxin transport and signaling and construct an interactive public website that will provide an integrated analysis of the data set. Our technology incorporated cell-specific polysome isolation and sequencing using the Solexa technology. In the first aim, we generated and confirmed the specificity of novel transgenic lines expressing tagged ribosomal protein in various cell types in the Arabidopsis primary root. We next crossed these lines to lines with targeted expression of BRI1 in the bri1 background. All lines were treated with BRs for two time points. The RNA-seq of their corresponding immunopurified polysomal RNA is nearly completed and the bioinformatic analysis of the data set will be completed this year. Followed, we will construct an interactive public website (our third aim). In the second aim we started revealing how spatio-temporalBR activity impinges on auxin transport in the Arabidopsis primary root. We discovered the unexpected role of BRs in controlling the expression of specific auxin efflux carriers, post-transcriptionally (Hacham et al, 2012). We also showed that this regulation depends on the specific expression of BRI1 in the epidermis. This complex and long term effect of BRs on auxin transport led us to focus on high resolution analysis of the BR signaling per se. Taking together, our ongoing collaboration and synergistic expertise (hormone action and plant development (IL) and whole-genome scale data analysis (US)) enabled the establishment of a powerful system that will tell us how distinct cell types respond to local and systemic BR signal. BR research is of special agriculture importance since BR application and BR genetic modification have been shown to significantly increase crop yield and to play an important role in plant thermotolerance. Hence, our integrated dataset is valuable for improving crop traits without unwanted impairment of unrelated pathways, for example, establishing semi-dwarf stature to allow increased yield in high planting density, inducing erect leaves for better light capture and consequent biomass increase and plant resistance to abiotic stresses.
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