Patched Together: cis-Regulatory Logic of the Hedgehog Response.

Abstract

Understanding the processes that control how we develop from a fertilized embryo to a functional adult is paramount for treating the diseases that result when these processes are disrupted at any stage of life. My dissertation investigates the cis-regulatory logic underlying how cell signaling pathways utilize the genome to create and maintain the wide variety of cell types and tissues needed for proper development and survival.

Surprisingly few cell signaling pathways are used throughout embryonic development; I have chosen to focus on Hedgehog (Hh) signaling, a pathway used in such diverse cellular contexts as digit specification, brain development, lung function, and reproductive maintenance. Disruption of this pathway results in developmental defects and cancer. It is essential to understand the mechanisms by which Hh signaling functions to treat these diseases more effectively. One relatively unexplored mechanism of Hh function is how its signal is transduced at the level of DNA, specifically through the regulation of gene expression. In this thesis, I explore the mechanisms that mediate tissue-specific, Hh-dependent gene regulation, and uncover an ancient cis-regulatory logic shared between flies and mice that has significant implications for the maintenance and evolution of cellular communication. I experimentally demonstrate that multiple enhancer elements, which control tissue-specific gene expression, rely on sub-optimal DNA sequences for binding of GLI proteins, the transcriptional effectors of Hh signaling. These sequences are essential to control gene expression in response to Hh and can influence the function of the pathway in a variety of cellular contexts. I also characterize several new transcriptional regulators of Hh signaling and introduce new tools to the field that allow for in depth analysis of the regulatory landscape of Hh target genes at any stage of development.

My work presented here addresses a significant gap in our knowledge of how the Hh signaling pathway functions at the cis-regulatory level and describes a framework by which new advances can be made on this topic in the future.