High resolution discovery of regulatory DNA with synthetic wild-type and ablated genome constructs
Name
1227278306-MIT.pdf
Size
1.51 MB
Format
Adobe PDF
Checksum (MD5)
028d0180aa363a109fe3c9bde53d4037
Author(s)
Holmes, Benjamin(Benjamin R.)
Advisor(s)
David K. Gifford.
Alternative Title
High resolution discovery of regulatory Deoxyribonucleic acid with synthetic wild-type and ablated genome constructs
Date Issued
2020
Publisher
Massachusetts Institute of Technology
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).
Subjects
Electrical Engineering and Computer Science.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
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.
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