Relevant bibliographies by topics / RNA splicing

Academic literature on the topic 'RNA splicing'

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Published: 4 June 2021
Last updated: 26 July 2024

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Journal articles on the topic "RNA splicing"

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van den Hoogenhof, Maarten M. G., Yigal M. Pinto, and Esther E. Creemers. "RNA Splicing." Circulation Research 118, no. 3 (February 5, 2016): 454–68. http://dx.doi.org/10.1161/circresaha.115.307872.

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Newman, Andy. "RNA splicing." Current Biology 8, no. 25 (December 1998): R903—R905. http://dx.doi.org/10.1016/s0960-9822(98)00005-0.

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Zong, Xinying, Vidisha Tripathi, and Kannanganattu V. Prasanth. "RNA splicing control." RNA Biology 8, no. 6 (November 2011): 968–77. http://dx.doi.org/10.4161/rna.8.6.17606.

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GUTHRIE, CHRISTINE. "Catalytic RNA and RNA Splicing." American Zoologist 29, no. 2 (May 1989): 557–67. http://dx.doi.org/10.1093/icb/29.2.557.

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Newman, Andy. "RNA enzymes for RNA splicing." Nature 413, no. 6857 (October 2001): 695–96. http://dx.doi.org/10.1038/35099665.

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David, Rachel. "Visualizing RNA splicing." Nature Reviews Molecular Cell Biology 14, no. 11 (October 23, 2013): 688. http://dx.doi.org/10.1038/nrm3689.

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Hryckiewicz, Katarzyna, Maciej Bura, Arleta Kowala-Piaskowska, Beata Bolewska, and Iwona Mozer-Lisewska. "HIV RNA splicing." HIV & AIDS Review 10, no. 3 (September 2011): 61–64. http://dx.doi.org/10.1016/j.hivar.2011.05.001.

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Koodathingal, Prakash, and Jonathan P. Staley. "Splicing fidelity." RNA Biology 10, no. 7 (July 2013): 1073–79. http://dx.doi.org/10.4161/rna.25245.

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Cordin, Olivier, and Jean D. Beggs. "RNA helicases in splicing." RNA Biology 10, no. 1 (January 2013): 83–95. http://dx.doi.org/10.4161/rna.22547.

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Einstein, Richard. "Splicing 2002: RNA splicing in human pathology." Pharmacogenomics 4, no. 1 (January 2003): 19–22. http://dx.doi.org/10.1517/phgs.4.1.19.22591.

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Dissertations / Theses on the topic "RNA splicing"

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Scadden, Alison Deirdre Jane. "Studies of RNA splicing and degradation." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627180.

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Källman, Annika. "Selective ADAR editing and the coordination with splicing /." Stockholm : Institutionen för molekylärbiologi och funktionsgenomik, Univ, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-302.

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Gonzàlez-Porta, Mar. "RNA sequencing for the study of splicing." Thesis, University of Cambridge, 2014. https://www.repository.cam.ac.uk/handle/1810/246596.

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Amongst the many processes that shape the final set of RNA molecules present in eukaryote cells, splicing emerges as the most prominent mechanism for message diversification. In recent years, applications of high throughput sequencing to RNA, known as RNA sequencing, have opened new avenues for the study of transcriptome composition, and have enabled further characterisation of such mechanism. In this thesis, I focus on the application of this technology to the study of human transcript diversity and its potential impact on the protein repertoire. In the first results chapter, I explore the extent of transcriptome diversity by asking whether there is a preference for the production of specific alternative transcripts within each given gene. I show that while many alternative transcripts can be detected, the expression of most protein coding genes tends to be dominated by one single transcript (major transcript). Such findings are validated in the second chapter, and are further used to explore changes in splicing patterns in a disease context. By analysing healthy and tumor samples from kidney cancer patients, I show that most of the detected splicing alterations do not lead to big changes in the relative abundance of major transcripts, at least in a recurrent manner. In addition, I introduce a framework to visualise the most extreme changes in splicing and to evaluate their potential functional impact. In the third chapter, I investigate the role of spliceosome assembly dynamics on the regulation of splice site choice. I show that depletion of PRPF8, a core spliceosomal component, leads to the preferential retention of a subset of introns with weaker splice sites, and also introduces alterations in the rate of co-transcriptional splicing. Finally, in the last chapter, I explore the validation of changes in alternative transcript abundance at the protein level, through the integration of results derived from RNA sequencing datasets with those obtained from proteomics experiments. Altogether, the findings described in this thesis provide a global picture on the extent of alternative splicing in the diversification of the transcriptome, expand current knowledge on the splicing reaction, and open new possibilities for the integration of transcriptomics and proteomics data.
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Friedman, Brad Aaron. "The evolution and specificity of RNA splicing." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/37139.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mathematics, 2006.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references (p. 119-125).
The majority of human genes are not encoded in contiguous segments in the genome but are rather punctuated by long interruptions known as introns. These introns are copied from generation to generation, and even from cell to cell as a person grows from an embryo into an adult. Each time a gene is activated, the cell must first accurately excise all the introns in a process known as splicing. This excision is determined by the sequence of the gene, but in a complicated way that is not fully understood. By analyzing gene sequences we can learn about how cells decide which sequences to splice. We have developed two new mathematical models, one for the end of introns, and another for long distance interactions between different parts of genes, that expose previously unknown elements potentially involved in the splicing reaction. However their boundaries are determined, introns are very ancient: although they are absent from bacteria they are found in almost all protists, fungi, plants and animals. It is therefore of great interest to explain their evolutionary origins. We have developed a probabilistic model for the evolution of introns and used it to perform a genome-wide analysis of the patterns of intron conservation in four euascomycete fungi, establishing that intron gain and loss are constantly reshaping the distribution of introns in genes.
by Brad Aaron Friedman.
Ph.D.
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Che, Austin 1979. "Engineering RNA logic with synthetic splicing ribozymes." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/47786.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.
Includes bibliographical references (p. 169-185).
Reusable components, such as logic gates and code libraries, simplify the design and implementation of electronic circuits and computer programs. The engineering of biological systems would benefit also from reusable components. In this thesis, I show the utility of splicing ribozymes for the biological engineer. Ribozymes allow the engineer to manipulate existing biological systems and to program self-modifying RNA systems. In addition, splicing ribozymes are easy to engineer, malleable, modular, and scalable. I used the model ribozyme from Tetrahymena to explore the principles behind engineering biological splicing systems in vivo. I show that the core ribozyme is modular and functions properly in many different contexts. Simple base pairing rules and computational RNA folding can predict splicing efficiency in bacterial cells. To test our understanding of the ribozyme, I generated synthetic ribozymes by manipulating the primary sequence while maintaining the secondary structure. Results indicate that our biochemical understanding of the ribozyme is accurate enough to support engineering. Splicing ribozymes can form core components in an all-RNA logic system. I developed biological transzystors, switches analogous to electrical transistors. Transzystors can use any trans-RNA as input and any RNA as output, allowing the genetic reading of RNA levels. I also show the ribozyme can write RNA using the trans-splicing reaction.
(cont.) Trans-splicing provides an easy mechanism to hook into an existing biological system and patch its operation. The generality of these ribozymes for a wide set of applications makes them promising tools for synthetic biology. Keywords: synthetic biology, RNA, Tetrahymena, ribozyme, splicing, transzystor.
by Austin J. Che.
Ph.D.
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Robinson, Robert Maxwell. "Splicing signals in Caenorhabditis elegans : candidate exonic splicing enhancer motifs /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/10846.

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Kosmidis, Tilemachos D. "Development of site-specific RNA labeling strategies to probe alternative RNA splicing." Thesis, University of Strathclyde, 2016. http://digitool.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=28492.

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The objective of this project was to develop a method for the labeling of RNA at specific locations using non-natural base pairs. This thesis details the efforts made towards this objective through the development of a modular synthetic platform for an expanded genetic alphabet and its evaluation using transcriptional assays. Chapter 1 introduces the structure and function of RNA, followed by a description of RNA processing events with emphasis placed on alternative RNA splicing and how aberrations in splicing can lead to disease. The concept of RNA labeling follows and examples from the literature are presented along with challenges associated with these techniques to elucidate key mechanistic splicing concepts. The concept of orthogonal base pairs is then introduced along with representative examples from the literature. The application of this concept in RNA labeling is then presented along with key examples from the literature. The limitations of these methods are highlighted followed by the specific aims behind this project. Chapter 2 presents the efforts made towards the development of a modular synthetic route for the synthesis of C-ribonucleosides, with a Heck reaction as the key step. Specifically, its application in the synthesis of the Z ribonucleoside developed by the Benner group is investigated. The chapter starts with re-introducing the Z/P pair developed by the Benner group and highlighting the reasons that placed it as our chosen base pair for RNA labeling. The synthesis of C-deoxyribonucleosides utilizing the Heck reaction is presented, followed by the challenges associated with C-ribonucleoside synthesis. The syntheses of the alkene and halide coupling partners of the proposed Heck reaction are firstly presented. Investigations on the Heck reaction are then presented, followed by investigations on the transformation of nitro group in Z to moieties suitable for further derivatization. The key outcome of this work is that a synthetic route involving the Heck reaction for the synthesis of C-ribonucleosidesis not feasible. This is due to long reaction times required to drive the Heck reaction to completion and difficulties encountered with elucidation of its stereselectivity. Furthermore, PCR experiments conducted by our collaborators within the Eperon group at the University of Leicester revealed significant misincorporation of Z opposite G. Consequently, a change in strategy towards the use of nucleotides developed by the Hirao group was made. Chapter 3 describes the development of a robust synthetic route for the synthesis of a library of C6-functionalized 2-aminopurines as potential candidates for an expanded genetic alphabet in RNA. The s/Pa pair developed by the Hirao group is re-introduced. The installation of an alkyne functionality on the guanosine scaffold via a Sonogashira reaction is described,followed by investigations of [3+2] cycloaddition reactions between the alkyne and azides or aldehyde oximes. Finally, the development of a novel Suzuki-Miyaura protocol for the direct installation of heterocyclic substituents on the guanosine scaffold is also reported. Key outcomes of this chapter are the following. A robust method was developed for the expedient synthesis of C6-functionalized s analogues. This method enabled access to various classes of analogues in three or six steps,including triazoles, isoxazoles, thiophenes and pyrazoles. Attempts to install an azide moiety to the guanosine were partly successful, but the strategy was abanonded due to reaction reproducibility issues. In addition, a C-H activation strategy was not successful on installing an oxazole moiety. Chapter 4 details the efforts towards the synthesis of nucleoside triphosphates based on the s analogues described in Chapter 3. This chapter will begin with the presentation of the most common strategies for the synthesis of nucleoside triphosphates. Initial attempts to synthesize triphosphates by global deprotection of nucleosides synthesized in Chapter 3 are next described. Attempts to install a silyl ether group in the 5’-OH are presented, followed by the installation of acetates on the 2’/3’ hydroxyls and attempts to protect the exocyclic amine on guanosine as the phenoxyacetamide. The installation of a pyrazole moiety via Suzuki-Miyauraprotocol using the corresponding boronic acid pinacol ester described in Chapter 3 is presented. The installation of an alkyne moiety is also described and the synthesis of an isoxazole analogue using this alkyne precursor will follow. The chapter will end with the presentation of the synthesis of pyrazole and isoxazole triphosphate analogues. The key outcome of this chapter is that employing different protecting groups on the 5’ and the 2’/3’ hydroxyls enabled the synthesis of pure triphosphates. Chapter 5 presents the evaluation of the nucleotide triphosphates synthesized in Chapter 4 regarding their transcriptional efficiency. Key outcome of this work are that high concentrations ( > 0.5 mM mM) are needed in order to observe significant incorporation of the analogues, compared to s, which needs 0.1 mM for efficient incorporation. At high concentration, the isoxazole moiety exhibits better incorporation efficiency compared to the pyrazole analogue. Furthermore, the addition of 0.5 mM of MnCl2 resulted in increased incorporation efficiency of the pyrazole analogue, while s and the isoxazole exhibited reduced efficiency under these conditions.
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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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Weinmeister, Robert. "Development of single-molecule methods for RNA splicing." Thesis, University of Leicester, 2014. http://hdl.handle.net/2381/29311.

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RNA splicing is an important step in the synthesis of most mammalian proteins and understanding the underlying molecular mechanisms is critical for tackling diseases linked to splicing. An important determinant is SRSF1, which has multiple roles in constitutive and alternative splicing. One of these roles is in the recognition and selection of 5’ splice sites due to an interaction with U1 snRNP during formation of complexes E and A. The exact roles and modes of interaction are not clear. Single-molecule methods are a key to understanding these. In this work, single-molecule methods were developed to investigate the number of bound proteins under different conditions. A home-built microscope utilising objective-based illumination by total internal reflection was used to look at these interactions at a single-molecule level and investigate the number of bound proteins under different conditions. The results showed that there was a distinctive reduction in the number of bound proteins in complex A, dependent on the availability of ATP. This was linked to the number of functional 5’ splice sites present, the U1 snRNP and phosphorylation. We could not find any evidence that sequences known to mediate stimulation by SRSF1 affect its binding. Using total internal reflection has inherent limitations, among them the necessary surface attachment and the dilutions required. These limitations could be overcome by the use of isolated microenvironments in the form of tiny droplets. A robust and convenient microfluidic device with a feature size of 3μm was set up and a suitable surfactant for biological samples was identified. Droplets with a diameter of 1μm were generated for the first time using flow focussing and single quantum dots and fluorescent proteins where identified within these droplets. The fluorescence intensity time traces from these droplets enabled the number of encapsulated fluorescent particles to be measured.
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Dickson, Alexa Megan. "Alternative RNA processing and strategies to modulate splicing." Diss., Columbia, Mo. : University of Missouri-Columbia, 2008. http://hdl.handle.net/10355/6057.

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Thesis (Ph. D.)--University of Missouri-Columbia, 2008.
The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Vita. "May 2008" Includes bibliographical references.
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Books on the topic "RNA splicing"

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1945-, Belfort Marlene, and Shub David A, eds. RNA: Catalysis, splicing, evolution. Amsterdam: Elsevier, 1989.

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D, Hames B., and Glover David M, eds. Transcription and splicing. Oxford, England: IRL Press, 1988.

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Yechiel, Becker, ed. Viral messenger RNA: Transcription, processing, splicing, and molecular structure. Boston: Nijhoff, 1985.

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J, Blencowe Benjamin, and Graveley Brenton R, eds. Alternative splicing in the postgenomic era. New York: Springer Science+Business Media, 2007.

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Johannes, Schenkel, ed. RNP particles, splicing, and autoimmune diseases. Berlin: Springer, 1998.

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Venables, Julian P. Alternative splicing in cancer. Trivandrum, Kerala, India: Transworld Research Network, 2006.

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Carstens, Russ P. Identification of RNA splicing errors resulting in human ornithine transcarbamylase deficiency. [New Haven: s.n.], 1990.

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Laboratory, Cold Spring Harbor, ed. Abstracts of papers presented at the 2003 meeting on eukaryotic mRNA processing, August 20-August 24, 2003. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory, 2003.

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Laboratory, Cold Spring Harbor, ed. Abstracts of papers presented at the 2005 meeting on Eukaryotic mRNA processing, August 24-August 28, 2005. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory, 2005.

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Lew, Jocelyne M. A CDKN1C mutation in Beckwith-Wiedemann syndrome patients reduces efficiency of RNA splicing. Ottawa: National Library of Canada, 2003.

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Book chapters on the topic "RNA splicing"

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Eger, Nicole, Laura Schoppe, Susanne Schuster, Ulrich Laufs, and Jes-Niels Boeckel. "Circular RNA Splicing." In Advances in Experimental Medicine and Biology, 41–52. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-13-1426-1_4.

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Huang, Xin-Yun, and David Hirsh. "RNA Trans-Splicing." In Genetic Engineering, 211–29. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4615-3424-2_12.

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Ribeca, Paolo, Vincent Lacroix, Michael Sammeth, and Roderic Guigó. "Analysis of RNA Transcripts by High-Throughput RNA Sequencing." In Alternative pre-mRNA Splicing, 544–54. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527636778.ch50.

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Ashraf, Tabasum, Humaira Shah, Rouf Maqbool, Auqib Manzoor, and Ashraf Dar. "Mechanism of RNA Splicing." In Alternative Splicing and Cancer, 24–46. Boca Raton: CRC Press, 2024. http://dx.doi.org/10.1201/9781003260394-2.

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Zhang, Zhaiyi, and Stefan Stamm. "Analysis of Mutations that Influence Pre-mRNA Splicing." In RNA, 137–60. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-59745-248-9_10.

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Kim, Young J. "Computational siRNA Design Considering Alternative Splicing." In RNA Interference, 81–92. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-588-0_5.

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Höbartner, Claudia. "Chemical Synthesis of RNA." In Alternative pre-mRNA Splicing, 154–62. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527636778.ch14.

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Cabianca, Daphne S., and Davide Gabellini. "RNA Interference (siRNA, shRNA)." In Alternative pre-mRNA Splicing, 164–73. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527636778.ch15.

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Bannikova, Olga, Maria Kalyna, and Andrea Barta. "Genomic SELEX to Identify RNA Targets of Plant RNA-Binding Proteins." In Alternative pre-mRNA Splicing, 218–26. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527636778.ch20.

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Boothroyd, J. C. "Trans-Splicing of RNA." In Nucleic Acids and Molecular Biology, 216–30. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-642-83709-8_14.

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Conference papers on the topic "RNA splicing"

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Jovanovic, Antonio, Israa Alqassem, Nathan Chappell, Stefan Canzar, and Domagoj Matijevic. "Predicting RNA splicing branchpoints." In 2022 45th Jubilee International Convention on Information, Communication and Electronic Technology (MIPRO). IEEE, 2022. http://dx.doi.org/10.23919/mipro55190.2022.9803685.

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Giaretta, Alberto, Khem Raj Ghusinga, and Timothy C. Elston. "A Stochastic model for RNA splicing." In 2022 European Control Conference (ECC). IEEE, 2022. http://dx.doi.org/10.23919/ecc55457.2022.9838423.

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Yoshida, Kenichi, Masashi Sanada, Yuichi Shiraishi, Daniel Nowak, Yasunobu Nagata, Ryo Yamamoto, Yusuke Sato, et al. "Abstract 5119: Frequent splicing pathway mutations and aberrant RNA splicing in myelodysplasia." 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.am2012-5119.

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Batyuchenko, A. V., A. A. Shishova, and A. V. Dereventsova. "POSSIBLE ROLE OF ALTERNATIVE SPLICING ENZYMES IN NON-REPLICATIVE RNA RECOMBINATION." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-230.

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RNA recombination is an important and one of the main mechanisms of RNA virus evolution. Two mechanisms of this process are currently known [2, 3]. A recombinant RNA molecule can be formed by replicative matrix switching [1, 2]. There is also increasing information about another non-replicative mechanism of viral RNA recombination [4]. However, the role of cellular factors in this process is still under investigation [2].
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Leclair, Nathan K., Laura Urbanski, Mattia Brugiolo, Marina Yurieva, Brenton R. Graveley, Albert Cheng, and Olga Anczukow. "Abstract 1147: RNA-targeting approaches to modulate alternative RNA splicing in cancer." In Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-1147.

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Chan, Alvin, Anna Korsakova, Yew-Soon Ong, Fernaldo Richtia Winnerdy, Kah Wai Lim, and Anh Tuan Phan. "RNA alternative splicing prediction with discrete compositional energy network." In ACM CHIL '21: ACM Conference on Health, Inference, and Learning. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3450439.3451857.

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Liu, Ruolin, and Julie Dickerson. "Computational methods for alternative splicing detection using RNA-seq." In BCB'13: ACM-BCB2013. New York, NY, USA: ACM, 2013. http://dx.doi.org/10.1145/2506583.2506666.

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Abo, Muthana Al, Steven R. Patierno, and Jennifer A. Freedman. "Abstract B061: Alternative RNA splicing and prostate cancer aggressiveness." In Abstracts: AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; December 2-5, 2017; Orlando, Florida. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.prca2017-b061.

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Phillips, Joshua, Jung-Hyun Kim, Sangbin Lim, Erin Ahn, and Ming Tan. "Abstract 1996: Regulation of RNA splicing of the ErbB family receptors by the splicing cofactor SON." 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.am2016-1996.

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Manchon, Laurent, Audrey Vautrin, Jamal Tazi, Aude Garcel, and Noelie Campos. "Targeting Long Non-Coding RNA splicing by novel candidate drug." In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2019. http://dx.doi.org/10.1109/bibm47256.2019.8982977.

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Reports on the topic "RNA splicing"

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Ostersetzer-Biran, Oren, and Alice Barkan. Nuclear Encoded RNA Splicing Factors in Plant Mitochondria. United States Department of Agriculture, February 2009. http://dx.doi.org/10.32747/2009.7592111.bard.

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Mitochondria are the site of respiration and numerous other metabolic processes required for plant growth and development. Increased demands for metabolic energy are observed during different stages in the plants life cycle, but are particularly ample during germination and reproductive organ development. These activities are dependent upon the tight regulation of the expression and accumulation of various organellar proteins. Plant mitochondria contain their own genomes (mtDNA), which encode for a small number of genes required in organellar genome expression and respiration. Yet, the vast majority of the organellar proteins are encoded by nuclear genes, thus necessitating complex mechanisms to coordinate the expression and accumulation of proteins encoded by the two remote genomes. Many organellar genes are interrupted by intervening sequences (introns), which are removed from the primary presequences via splicing. According to conserved features of their sequences these introns are all classified as “group-II”. Their splicing is necessary for organellar activity and is dependent upon nuclear-encoded RNA-binding cofactors. However, to-date, only a tiny fraction of the proteins expected to be involved in these activities have been identified. Accordingly, this project aimed to identify nuclear-encoded proteins required for mitochondrial RNA splicing in plants, and to analyze their specific roles in the splicing of group-II intron RNAs. In non-plant systems, group-II intron splicing is mediated by proteins encoded within the introns themselves, known as maturases, which act specifically in the splicing of the introns in which they are encoded. Only one mitochondrial intron in plants has retained its maturaseORF (matR), but its roles in organellar intron splicing are unknown. Clues to other proteins required for organellar intron splicing are scarce, but these are likely encoded in the nucleus as there are no other obvious candidates among the remaining ORFs within the mtDNA. Through genetic screens in maize, the Barkan lab identified numerous nuclear genes that are required for the splicing of many of the introns within the plastid genome. Several of these genes are related to one another (i.e. crs1, caf1, caf2, and cfm2) in that they share a previously uncharacterized domain of archaeal origin, the CRM domain. The Arabidopsis genome contains 16 CRM-related genes, which contain between one and four repeats of the domain. Several of these are predicted to the mitochondria and are thus postulated to act in the splicing of group-II introns in the organelle(s) to which they are localized. In addition, plant genomes also harbor several genes that are closely related to group-II intron-encoded maturases (nMats), which exist in the nucleus as 'self-standing' ORFs, out of the context of their cognate "host" group-II introns and are predicted to reside within the mitochondria. The similarity with known group-II intron splicing factors identified in other systems and their predicted localization to mitochondria in plants suggest that nuclear-encoded CRM and nMat related proteins may function in the splicing of mitochondrial-encoded introns. In this proposal we proposed to (i) establish the intracellular locations of several CRM and nMat proteins; (ii) to test whether mutations in their genes impairs the splicing of mitochondrial introns; and to (iii) determine whether these proteins are bound to the mitochondrial introns in vivo.
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Iczkowski, Kenneth A. Alternate Splicing of CD44 Messenger RNA in Prostate Cancer Growth. Fort Belvoir, VA: Defense Technical Information Center, April 2008. http://dx.doi.org/10.21236/ada483366.

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Iczkowski, Kenneth A., Eric W. Robbins, Kui Yang, Alina Handorean, and Yaqiong Tang. Alternate Splicing of CD44 Messenger RNA in Prostate Cancer Growth. Fort Belvoir, VA: Defense Technical Information Center, October 2009. http://dx.doi.org/10.21236/ada525215.

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Fluhr, Robert, and Volker Brendel. Harnessing the genetic diversity engendered by alternative gene splicing. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7696517.bard.

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Our original objectives were to assess the unexplored dimension of alternative splicing as a source of genetic variation. In particular, we sought to initially establish an alternative splicing database for Arabidopsis, the only plant for which a near-complete genome has been assembled. Our goal was to then use the database, in part, to advance plant gene prediction programs that are currently a limiting factor in annotating genomic sequence data and thus will facilitate the exploitation of the ever increasing quantity of raw genomic data accumulating for plants. Additionally, the database was to be used to generate probes for establishing high-throughput alternative transcriptome analysis in the form of a splicing-specific oligonucleotide microarray. We achieved the first goal and established a database and web site termed Alternative Splicing In Plants (ASIP, http://www.plantgdb.org/ASIP/). We also thoroughly reviewed the extent of alternative splicing in plants (Arabidopsis and rice) and proposed mechanisms for transcript processing. We noted that the repertoire of plant alternative splicing differs from that encountered in animals. For example, intron retention turned out to be the major type. This surprising development was proven by direct RNA isolation techniques. We further analyzed EST databases available from many plants and developed a process to assess their alternative splicing rate. Our results show that the lager genome-sized plant species have enhanced rates of alternative splicing. We did advance gene prediction accuracy in plants by incorporating scoring for non-canonical introns. Our data and programs are now being used in the continuing annotation of plant genomes of agronomic importance, including corn, soybean, and tomato. Based on the gene annotation data developed in the early part of the project, it turned out that specific probes for different exons could not be scaled up to a large array because no uniform hybridization conditions could be found. Therefore, we modified our original objective to design and produce an oligonucleotide microarray for probing alternative splicing and realized that it may be reasonable to investigate the extent of alternative splicing using novel commercial whole genome arrays. This possibility was directly examined by establishing algorithms for the analysis of such arrays. The predictive value of the algorithms was then shown by isolation and verification of alternative splicing predictions from the published whole genome array databases. The BARD-funded work provides a significant advance in understanding the extent and possible roles of alternative splicing in plants as well as a foundation for advances in computational gene prediction.
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Levy, Avraham A., and Virginia Walbot. Regulation of Transposable Element Activities during Plant Development. United States Department of Agriculture, August 1992. http://dx.doi.org/10.32747/1992.7568091.bard.

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We have studied the regulation of the maize Ac and MuDR transposable elements activities during plant development. Ac was studied in an heterologous system (transgenic tobacco plants and cell suspensions) while MuDR was studied in the native maize background. The focus of this study was on the transcriptional regulation of Ac and MuDR. For Ac, the major achievements were to show that 1-It is autoregulated in a way that the Ac-encoded transposase can repress the activity of its own promoter; 2-It is expressed at low basal level in all the plant organs that were studied, and its activity is stronger in dividing tissues -- a behaviour reminiscent of housekeeping genes; 3- the activity of Ac promoter is cell cycle regulated -- induced at early S-phase and increasing until mitosis; 4- host factor binding sites were identified at both extremities of Ac and may be important for transposition. For MuDR, It was shown that it encodes two genes, mudrA and mudrB, convergently transcribed from near-identical promoters in the terminal inverted repeats. Distinct 5' start sites, alternative splicing, production of antisense RNA and tissue specificity were all shown to be involved in the regulation of MuDR.
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Schuster, Gadi, and David Stern. Integrated Studies of Chloroplast Ribonucleases. United States Department of Agriculture, September 2011. http://dx.doi.org/10.32747/2011.7697125.bard.

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Gene regulation at the RNA level encompasses multiple mechanisms in prokaryotes and eukaryotes, including splicing, editing, endo- and exonucleolytic cleavage, and various phenomena related to small or interfering RNAs. Ribonucleases are key players in nearly all of these post-transcriptional mechanisms, as the catalytic agents. This proposal continued BARD-funded research into ribonuclease activities in the chloroplast, where RNase mutation or deficiency can cause metabolic defects and is often associated with plant chlorosis, embryo or seedling lethality, and/or failure to tolerate nutrient stress. The first objective of this proposal was to examined a series of point mutations in the PNPase enzyme of Arabidopsis both in vivo and in vitro. This goal is related to structure-function analysis of an enzyme whose importance in many cellular processes in prokaryotes and eukaryotes has only begun to be uncovered. PNPase substrates are mostly generated by endonucleolytic cleavages for which the catalytic enzymes remain poorly described. The second objective of the proposal was to examine two candidate enzymes, RNase E and RNase J. RNase E is well-described in bacteria but its function in plants was still unknown. We hypothesized it catalyzes endonucleolytic cleavages in both RNA maturation and decay. RNase J was recently discovered in bacteria but like RNase E, its function in plants had yet to be explored. The results of this work are described in the scientific manuscripts attached to this report. We have completed the first objective of characterizing in detail TILLING mutants of PNPase Arabidopsis plants and in parallel introducing the same amino acids changes in the protein and characterize the properties of the modified proteins in vitro. This study defined the roles for both RNase PH core domains in polyadenylation, RNA 3’-end maturation and intron degradation. The results are described in the collaborative scientific manuscript (Germain et al 2011). The second part of the project aimed at the characterization of the two endoribonucleases, RNase E and RNase J, also in this case, in vivo and in vitro. Our results described the limited role of RNase E as compared to the pronounced one of RNase J in the elimination of antisense transcripts in the chloroplast (Schein et al 2008; Sharwood et al 2011). In addition, we characterized polyadenylation in the chloroplast of the green alga Chlamydomonas reinhardtii, and in Arabidopsis (Zimmer et al 2009). Our long term collaboration enabling in vivo and in vitro analysis, capturing the expertise of the two collaborating laboratories, has resulted in a biologically significant correlation of biochemical and in planta results for conserved and indispensable ribonucleases. These new insights into chloroplast gene regulation will ultimately support plant improvement for agriculture.
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Ozias-Akins, P., and R. Hovav. molecular dissection of the crop maturation trait in peanut. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134157.bard.

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Crop maturation is one of the most recognized characteristics of peanut, and it is crucial for adaptability and yield. However, not much is known regarding its genetic and molecular control. The goals of this project were to study the molecular-genetic components that control crop maturation in peanut and identify candidate genes. Crop maturation was studied directly by phenotyping the maturity level or through other component traits such as flowering pattern and branching habit. Six different RIL populations (HH, RR, CC, FNC, TGT and FLIC) were used for the genetic analysis. In total, 14 QTLs were found for maturity level. The phenotypic explanation values ranged in 5.3%-18.6%. Common QTL were found between maturity level and harvest index (in RR and CC populations), branching habit (in HH population), flowering pattern/branching rate (in CC and TGT populations) and pod size (in CC population). Further investigations were done to define genes that control maturity level and the component traits. A map-based cloning approach was used to identify a major candidate gene for branching habit - a novel AhMADS-box gene (AhMADS). AhMADS was mainly expressed in the lateral shoot, the organ in which the difference between branching habit occurs. Sequence alignment analysis found SNPs in AhMADS that cause to exon/intron splicing alterations. Overexpression study of AhMADs-box in tobacco under 35S control revealed one line with a spreading-like lateral shoot indicating that AhMADS may be the causing effect of BH and therefore indirectly controls maturity level. In addition, several candidate genes were defined that may control flowering pattern. An RNA expression study was performed on two parental lines, Tifrunner and GT-C20, identifying four candidate genes in the flowering regulatory pathway that were down-regulated at the mainstem (non-flowering) compared to the first (flowering) shoot, indicating their influence on flowering pattern. Also, another candidate gene was identified, Terminal Flowering 1-like (AhTFL1), which was located within a small segment in chromosome B02. A 1492 bp deletion was found in AhTFL1 that completely co-segregates with the flowering pattern phenotype in the CC population and two independent EMS-mutagenized M2 families. AhTFL1 was significantly less expressed in flowering than non-flowering branches. Finally, a field trial showed that an EMS line (B78) mutagenized in AhTFL1 is ~18% days earlier than the control (Hanoch). In conclusion, our study revealed new insights into the molecular basis for the fundamentally important crop maturity trait in peanut. The results generated new information and materials that will promote informed targeting of peanut idiotypes by indirect selection and genomic breeding approaches.
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