Abstract

The control of cellular state has many promising applications, including stem cell biology andregenerative medicine, biofuel production, and gene therapy. This dissertation demonstrates acomprehensive approach to cellular state control at the transcriptional level. We introduce anovel algorithm, NetSurgeon, which utilizes genome-wide gene regulatory networks to identifyinterventions that will force a cell toward a desired expression state. Following extensive insilico validation, we applied NetSurgeon to S. cerevisiae biofuel production, generatinginterventions designed to promote a fermentative state during xylose catabolism. Our selectedinterventions successfully promoted a fermentative transcriptional state and generated strainswith higher xylose import rates, improved xylose integration and increased ethanol productionrates. We then step down to a single gene level and exhibit a cis-engineering strategy thatenables precise expression control. We demonstrate that synthetic promoters can be functionallydecomposed into individual components that can be characterized in isolation and used to train acomposite model capable of predicting the action of the full system. These findings representsignificant progress towards the insertion of orthogonal control circuits into the cell for thecontrol of gene expression. Taken together, this dissertation represents an integrative process ofquantitative measurement, modeling, and intervention that comprehensively examines methodsfor cellular state control at the genome-wide and gene levels.

Committee Chair

Michael R Brent

Committee Members

Thomas Baranski, Barak Cohen, Gautam Dantas, James Havranek, Joseph Jez

Comments

Permanent URL: https://doi.org/10.7936/K77942V2

Degree

Doctor of Philosophy (PhD)

Author's Department

Biology & Biomedical Sciences (Molecular Cell Biology)

Author's School

Graduate School of Arts and Sciences

Document Type

Dissertation

Date of Award

Spring 5-15-2015

Language

English (en)

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