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Alternative isoform regulation in myotonic dystrophy

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dc.contributor.advisor Christopher B. Burge and David E. Housman. en_US Wang, Eric T. (Eric Tzy-shi) en_US
dc.contributor.other Harvard--MIT Program in Health Sciences and Technology. en_US 2012-05-15T21:14:47Z 2012-05-15T21:14:47Z 2012 en_US 2012 en_US
dc.description Thesis (Ph. D.)--Harvard-MIT Program in Health Sciences and Technology, 2012. en_US
dc.description Cataloged from PDF version of thesis. en_US
dc.description Includes bibliographical references. en_US
dc.description.abstract Myotonic dystrophy (DM) is the most common form of adult onset muscular dystrophy, affecting more than 1 in 8000 individuals globally. The symptoms of DM are multi-systemic and include myotonia, severe muscle wasting, cardiac arrhythmias, cataracts, gastrointestinal dysfunction, and cognitive deficits. DM is caused by the expansion of CTG or CCTG repeat sequences expressed in noncoding portions of RNA, which sequester or activate RNA splicing factor proteins, leading to widespread deleterious changes in transcriptome isoform usage. We developed a method for studying transcriptomes, RNAseq, which provides a high resolution, digital inventory of gene and isoform expression. By applying RNAseq to human tissues and cell lines, we discovered that essentially 92-94% of all human genes are alternatively spliced, 86% of them with a minor isoform frequency 15% or more. We found that the majority of alternative splicing and alternative polyadenylation and cleavage events are tissue-regulated, and that patterns of these RNA processing events are strongly correlated across tissues, implicating protein factors that may regulate both types of events. We applied this method towards the goal of identifying transcriptome changes occurring in DM, focusing on the Muscleblind-like (MBNL) family of RNA binding proteins, which are functionally inactivated by CUG or CCUG repeats. Using RNAseq to profile tissues and cells depleted of MBNLs, we found that MBNL1 and MBNL2 co-regulate hundreds of redundant targets. MBNL1 UV cross-linking and immunoprecipitation, followed by sequencing (CLIPseq), was used to identify the in vivo transcriptome-wide binding locations of MBNL1, and facilitated the construction of a context-dependent RNA map for MBNL1 splicing regulation. Extensive 3' UTR binding of MBNL1 was found to localize mRNAs to membrane compartments of mouse myoblasts, suggesting a new global function for MBNLs, and additional mechanisms by which MBNL depletion can lead to DM symptoms. en_US
dc.description.statementofresponsibility by Eric T. Wang. en_US
dc.format.extent 194 p. 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 en_US
dc.subject Harvard--MIT Program in Health Sciences and Technology. en_US
dc.title Alternative isoform regulation in myotonic dystrophy en_US
dc.type Thesis en_US Ph.D. en_US
dc.contributor.department Harvard--MIT Program in Health Sciences and Technology. en_US
dc.identifier.oclc 792948545 en_US

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