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Functional and computational analysis of RNA-binding proteins and their roles in cancer

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dc.contributor.advisor Christopher B. Burge and Rudolf Jaenisch. en_US
dc.contributor.author Katz, Yarden en_US
dc.contributor.other Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences. en_US
dc.date.accessioned 2014-09-19T19:38:16Z
dc.date.available 2014-09-19T19:38:16Z
dc.date.copyright 2014 en_US
dc.date.issued 2014 en_US
dc.identifier.uri http://hdl.handle.net/1721.1/89864
dc.description Thesis: Ph. D., Massachusetts Institute of Technology, Department of Brain and Cognitive Sciences, 2014. en_US
dc.description This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. en_US
dc.description Cataloged from student-submitted PDF version of thesis. en_US
dc.description Includes bibliographical references (pages 197-200). en_US
dc.description.abstract This work is concerned with mRNA processing in mammalian cells and proceeds in two parts. In the first part, I introduce a computational framework for inferring the abundances of mRNA isoforms using high-throughput RNA sequencing data. This framework was applied to study the targets of the ubiquitous splicing factor hnRNP H in human cells. In the second part, I describe an experimental study of the Musashi (hnRNP-like) family of RNA-binding proteins in stem cells and cancer cells, which incorporates computational analyses that rely heavily on the framework developed in part one. In sum, this work provides a computational framework of general use in global analyses of RNA processing and its protein regulators, as well as functional insights into a family of poorly understood RNA-binding proteins. Several related analyses and techniques developed as part of the thesis are described in Appendix A-C. Appendix A describes a study of activity-dependent gene expression and mRNA processing in the mouse olfactory bulb. It uses computational techniques developed in part one of the thesis. Appendix B describes a technique for quantitative visualization of alternative splicing from RNA sequencing data and its integration into a genome browser. Appendix C describes a method for clonal analysis of neural stem cell growth and differentiation in culture using live imaging and `microdot' plates, developed as part of the work presented in part one of the thesis. en_US
dc.description.statementofresponsibility by Yarden Katz. en_US
dc.format.extent 241 pages en_US
dc.language.iso eng en_US
dc.publisher Massachusetts Institute of Technology en_US
dc.rights M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. en_US
dc.rights.uri http://dspace.mit.edu/handle/1721.1/7582 en_US
dc.subject Brain and Cognitive Sciences. en_US
dc.title Functional and computational analysis of RNA-binding proteins and their roles in cancer en_US
dc.type Thesis en_US
dc.description.degree Ph. D. en_US
dc.contributor.department Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences. en_US
dc.identifier.oclc 890196965 en_US


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