2026-09-20T10:21:46Zhttps://dspace.mit.edu/server/oai/request

oai:dspace.mit.edu:1721.1/728222022-01-13T07:54:15Zcom_1721.1_7582com_1721.1_7581col_1721.1_131023

Christopher B. Burge. Hamilton, Monica L. (Monica Lauren) Massachusetts Institute of Technology. Dept. of Biology. Massachusetts Institute of Technology. Department of Biology 2012-09-13T18:54:01Z 2012-09-13T18:54:01Z 2012 2012 http://hdl.handle.net/1721.1/72822 806953128 Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Biology, 2012. Cataloged from PDF version of thesis. Includes bibliographical references (p. 21-23). Exon scrambling is a phenomenon in which the exons of an mRNA transcript are spliced in an order inconsistent with that of the genome. In this thesis, I present a computational analysis of scrambled exons in human and mouse. RNA-seq data was mapped to the genome and all unaligned reads were subsequently mapped to a database of all possible exon-exon junctions. Eight conserved genes were found to undergo scrambled splicing in both species. In several cases, not only the gene was conserved, but the particular exons involved were conserved as well. Reading frame was preserved in just over half of the events, indicating that although some transcripts may be translated into protein, some may be non-functional or may play a regulatory role. The introns flanking scrambled exons were significantly longer than average, providing clues to the mechanism for this abnormal splicing pattern. The results of this study demonstrate that presence of scrambled transcripts in the cell is infrequent, but can be conserved over tens of millions of years of evolution, suggesting it has a biological function. by Monica L. Hamilton. S.M. 36 p. eng Massachusetts Institute of Technology 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. http://dspace.mit.edu/handle/1721.1/7582 Biology. Conservation of exon scrambling in human and mouse Thesis application/pdf Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="df7dbf21-9320-4e0e-9f2f-a2f8217623f8"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>Conservation of exon scrambling in human and mouse</Title> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2012</PublicationDate> <Authors> <Author> <DisplayName>Hamilton, Monica L. (Monica Lauren)</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Biology.</Keyword> <Abstract>Exon scrambling is a phenomenon in which the exons of an mRNA transcript are spliced in an order inconsistent with that of the genome. In this thesis, I present a computational analysis of scrambled exons in human and mouse. RNA-seq data was mapped to the genome and all unaligned reads were subsequently mapped to a database of all possible exon-exon junctions. Eight conserved genes were found to undergo scrambled splicing in both species. In several cases, not only the gene was conserved, but the particular exons involved were conserved as well. Reading frame was preserved in just over half of the events, indicating that although some transcripts may be translated into protein, some may be non-functional or may play a regulatory role. The introns flanking scrambled exons were significantly longer than average, providing clues to the mechanism for this abnormal splicing pattern. The results of this study demonstrate that presence of scrambled transcripts in the cell is infrequent, but can be conserved over tens of millions of years of evolution, suggesting it has a biological function.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>