Date of Degree


Document Type


Degree Name





Mark Emerson

Committee Members

Bao Vuong

Cesar Arenas-Mena

Matthew Rockman

Michael Verzi

Subject Categories

Developmental Biology | Developmental Neuroscience | Genomics


retinal development, cone photoreceptors, horizontal cells, cell fate restriction, comparative development


The diverse neuronal cell types in the vertebrate retina all originate from multipotent retinal progenitor cells (RPCs). These undergo a series of molecular changes driven by developmental gene regulatory networks (GRNs) as they divide to generate RPCs which are more restricted in their potential fates. It is crucial to understand these GRNs and changes to gene expression in order to understand how cell identity is established during retinal development. In particular, the GRN that promotes the development of cone photoreceptors and horizontal cells is not well-defined. This work focuses on two approaches to further elucidate the components of this regulatory network and how gene expression is controlled in developing cones and horizontal cells.

The first part of this work is largely focused on a fate-restricted RPC that can be defined by the activity of the cis-regulatory element ThrbCRM1 and preferentially generates cone photoreceptors and horizontal cells. This element is bound by two transcription factors: Otx2 and Onecut1. To identify upstream factors that contribute to Onecut1 expression in this population, this work used a large-scale enhancer screen which yielded two regulatory elements: Onecut1 ECR65 and Onecut1 ECR9. These enhancers are both active in ThrbCRM1-positive cells and mark populations that are biased to the cone photoreceptor and horizontal cell fates. Through a combination of bioinformatic tools for predictive binding and functional experiments, it was shown that both of these elements respond to bHLH family transcription factors. Theseexperiments provide evidence that bHLH expression is involved in restricting RPCs to the cone and horizontal cell fates.

The second part of this work describes a comparative study between cone-dominant and rod-dominant mammalian retinae, using the thirteen-lined ground squirrel and mouse. This work is the first to describe retinal development in the thirteen-lined ground squirrel retina and demonstrates differences in the timing of particular events in cone and horizontal cell development. This work also used ATAC-seq to compare developmental chromatin accessibility between mouse and ground squirrel retinae. This approach led to the identification of several differentially accessible chromatin regions, some near known cone photoreceptor and horizontal cell genes. This work provides the tools needed to further understand the gene regulatory differences between the developing mouse and ground squirrel retinae. This comparative approach can elucidate how the ground squirrel retina promotes the cone and horizontal cell fates.