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High resolution discovery of regulatory DNA with synthetic wild-type and ablated genome constructs

Author(s)
Holmes, Benjamin(Benjamin R.)
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Download1227278306-MIT.pdf (1.511Mb)
Alternative title
High resolution discovery of regulatory Deoxyribonucleic acid with synthetic wild-type and ablated genome constructs
Other Contributors
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science.
Advisor
David K. Gifford.
Terms of use
MIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided. http://dspace.mit.edu/handle/1721.1/7582
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Abstract
Genomic enhancer elements play a role in modulating gene expression by interacting with effector proteins known as transcription factors. We present a new computational method, "STARR-scan", which identifies transcription factor motif appearances in synthetic DNA constructs that are correlated with enhancer activity. Using a tiled STARR-seq assay, we demonstrate that STARR-scan can suggest the biological function of transcription factors previously suspected to activate the APOBEC-3B gene. Using the same methodology, STARR-scan can suggest transcription factors with previously unknown biological activity which may regulate the APOBEC-3B gene. These novel factors may have biological significance in our understanding of cancer biology.
Description
Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, September, 2020
 
Cataloged from student-submitted PDF version of thesis.
 
Includes bibliographical references (pages 22-23).
 
Date issued
2020
URI
https://hdl.handle.net/1721.1/129182
Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Publisher
Massachusetts Institute of Technology
Keywords
Electrical Engineering and Computer Science.

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