This item is under embargo and not available online per the author's request. For access information, please visit

Date of Award

Spring 5-15-2018

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Genetics & Genomics)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



For decades, studies of the genetic basis of disease have focused on rare coding mutations that disrupt protein function, leading to the identification of hundreds of genes underlying Mendelian diseases. However, many complex diseases are non-Mendelian, and less than 2% of the genome is coding. It is now clear that non-coding variants contribute to disease susceptibility, but the precise underlying mechanisms are generally unknown. Cis-regulatory elements (CREs) are transcription factor (TF)-bound genomic regions that regulate gene expression, and variants within CREs can therefore modify gene expression. The putative locations of CREs in a variety of cell types have been identified through genome-wide assays of TF binding and epigenomic signatures, providing a starting point for probing the effects of cis-regulatory variants. Unlike coding mutations, which can be interpreted based on the genetic code, the functional consequence of any given cis-regulatory variant is difficult to predict even at the molecular level. Therefore, a major bottleneck lies in interpreting the functional significance of these variants.

In the present work, I study the effects of cis-regulatory variants in the central nervous system (CNS), specifically in retina and brain. The retina is composed of well-characterized neuronal cell types and an extensively studied transcriptional network, while the brain is the center of human cognition and a target of devastating neuropsychiatric diseases. First, I take advantage of the genetic diversity between two distantly related mouse strains to describe the relationship between cis-regulatory variants and differences in retinal gene expression. I identify cis- and trans-regulatory effects, as well as parent-of-origin effects. Second, I develop a new technology based on an existing massively parallel reporter assay, CRE-seq, to enable the functional study of long CREs in the CNS in vivo for the first time. I demonstrate the ability of this approach to measure tissue-specific cis-regulatory activity in the brain and to pinpoint DNA bases critical for activity. Finally, I conduct a detailed mechanistic study of a non-coding region containing variants associated with both human cognitive performance and bipolar disorder. This last study illustrates the complexities and challenges of establishing the causal role of non-coding variants in disease.


English (en)

Chair and Committee

Joseph C. Corbo

Committee Members

Shiming Chen, Donald F. Conrad, Joseph D. Dougherty, Justin C. Fay,


Permanent URL:

Available for download on Friday, March 13, 2020