Multiplex genome editing and gene regulation in eukaryotic cells

Biological functions of a cell are encoded within its genome and regulated through complex genetic networks. Direct manipulation of the genome and the transcriptome in multiplex enables study of gene-gene interactions and rapid creation of industrially or therapeutically useful cells. Such manipulations, including genome editing and epigenetic regulation of gene expression, rely on a group of precise DNA-binding proteins, which include zinc finger proteins (ZFPs), transcription activator like effectors (TALEs), and clustered, regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9). ZFPs and TALEs rely on protein domain shuffling for targeting different genomic loci, which can be laborious and expensive. Instead, CRISPR/Cas9 is guided by a 20 bp ribonucleotide, which can be synthesized in multiplex rapidly and cost-effectively. This dissertation describes my efforts in engineering the CRISPR/Cas9 system for multiplex genome editing and gene regulation in eukaryotic cells. The first part of this dissertation (Chapters 2 and 3) focuses on genome editing in Saccharomyces cerevisiae. S. cerevisiae, also known as the baker’s yeast, is an important model eukaryotic organism for basic research, as well as a preferred industrial host for production of biofuels, pharmaceuticals and fine chemicals. I developed a Homology-Integrated CRISPR/Cas9 (HI-CRISPR) system for concurrent disruption of up to three genes in S. cerevisiae. This system enabled rapid and efficient generation of yeast strains with multiple mutations and should prove useful for studying yeast gene functions. Based on the design of the HI-CRISPR system, I further developed a CRISPR/Cas9 and homology-directed repair assisted genome-scale engineering (CHAnGE) system for engineering and directed evolution of S. cerevisiae strains. Using the CHAnGE system, I identified both known and novel genes susceptible to acetic acid or furfural toxicity. Finally, I demonstrated one-step, high efficiency in vivo site directed mutagenesis in S. cerevisiae for introducing designed mutations into native chromosomal contexts. The second part of this dissertation (Chapters 4 and 5) focuses on ligand-inducible, multiplex gene regulation in mammalian cells. Ligand-inducible gene regulation enables temporal control of gene functions, which is necessary in interrogating dynamic gene regulatory networks. However, temporal control is currently limited on a single gene level. I developed chemically induced transcription activators by combining orthogonal CRISPR/Cas9 systems and chemically induced dimerizing proteins. In HEK293T cells, these transcription activators exerted simultaneous activation of multiple genes and orthogonal regulation of different genes in a ligand-dependent manner with minimal background. As proof of concept, I attempted to convert mouse embryonic fibroblasts to neuronal cells using chemically induced CRISPR/Cas9 activators.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biochemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2017

Author dc:creator

• Bao, Zehua

Contributors dc:contributor

• Zhao, Huimin
• Morrissey, James H.
• Chen, Jie
• Zhang, Kai

• Genome editing
• Genome engineering
• Gene regulation
• Clustered, regularly interspaced short palindromic repeats (CRISPR)
• Cas9
• Saccharomyces cerevisiae

Statement dc:rights

• Copyright 2017 Zehua Bao

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/97547

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F97547