High resolution discovery of regulatory DNA with synthetic wild-type and ablated genome constructs
Author(s)Holmes, Benjamin(Benjamin R.)
High resolution discovery of regulatory Deoxyribonucleic acid with synthetic wild-type and ablated genome constructs
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science.
David K. Gifford.
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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.
Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, September, 2020Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 22-23).
DepartmentMassachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Massachusetts Institute of Technology
Electrical Engineering and Computer Science.