Date of Award
7-5-2024
Degree Name
Doctor of Philosophy (PhD)
Degree Type
Dissertation
Abstract
Precise gene expression programs are foundational to organism development and homeostasis. Transcription factors play a central role in establishing and maintaining these programs. Large-scale transcriptomic studies have generated parts lists of transcription factors. However, these descriptive works rarely formulate a cohesive model of how these transcription factors work together to support a functional organism. Mutations that affect transcription factor functions can lead to a broad range of human diseases. Therefore, it is crucial to understand the principles that transcription factors achieve spatial, temporal, and quantitative precision in their regulated gene expression programs. I have investigated transcriptional regulation in rod and cone photoreceptors. Photoreceptors are specialized neurons in the retina that function in the initial step of vision. Development and maintenance of photoreceptors are regulated by a gene regulatory network that revolves around a homeodomain transcription factor (HD TF) encoded by the Cone-rod homeobox (CRX) gene. CRX regulates photoreceptor gene expression by recognizing specific HD DNA motifs in the genome. The conventional model of the CRX function posits that it binds one type of consensus DNA motif. However, human mutations in CRX HD are associated with distinct blinding diseases, suggesting complex modes of CRX HD-DNA interactions and differential perturbations by disease-associated mutations. My thesis project aims to establish quantitative models to understand the features of CRX HD-DNA interactions in photoreceptor development and diseases. I have focused my research on two CRX HD missense mutations, p.E80A (E80A) and p.K88N (K88N), that are associated with dominant Cone-rod dystrophy (CoRD) and dominant Leber congenital amaurosis (LCA) in humans. Using an integrated approach that combines quantitative in vitro biochemical models, functional genomics, cellular profiling, and functional testing in mutation knock-in mouse models, I identified two novel gain-of-function pathogenic mechanisms. I found that E80A and K88N differentially alter CRX HD-DNA binding specificity and cooperativity, leading to distinct photoreceptor developmental deficits in mutant mouse retinas recapitulating human conditions. By comparing the epigenome and transcriptome dynamics in WT and Crx mutant retinas, I uncovered an underappreciated role of differential CRX interactions with subtypes of HD motifs in regulating stage and cell-type specific chromatin remodeling and temporal gene regulation during photoreceptor development. Collectively, my study refines the CRX mechanistic model in photoreceptor development, expands our knowledge of the diverse mechanisms that CRX mutations lead to severe, dominant retinopathies, and lays the foundation for the future development of therapeutic strategies targeting different pathogenic mechanisms. Beyond CRX, my study affords insights into the intricate mechanisms that transcription factors deploy to achieve precision and functional specificity in regulating diverse biology processes. Moreover, the holistic approach in my study offers a transferable framework for the mechanistic studies of transcription factors in other cell types and their associated diseases.
Language
English (en)
Chair and Committee
Shiming Chen
Committee Members
Barak Cohen; Brian Clark; Gary Stormo; Joseph Dougherty
Recommended Citation
Zheng, Yiqiao, "Transcriptional precision in photoreceptor development and diseases - Lessons from the retinal transcription factor CRX" (2024). Arts & Sciences Electronic Theses and Dissertations. 3328.
https://openscholarship.wustl.edu/art_sci_etds/3328