Identification of transcription factors involved in the specification of photoreceptor subtypes

During development, retinal progenitors navigate a complex landscape of fate decisions that results in the generation of unique cell types necessary for proper vision. Here, we aim to provide the resources and techniques required to identify fac-tors that are critical for fate decisions in photoreceptors. These factors help create a diversity of photoreceptor subtypes that sustain vision in day and night, enable the discrimination of colors, facilitate the detection of prey and predators, and support other aspects of vision. First, we generate a key resource: a high-quality and deep transcriptomic profile of each photoreceptor subtype in zebrafish. We make this resource openly accessible, easy to explore and integrate it with other currently available photoreceptor transcriptomic datasets. Second, using our transcriptomic profiles, we derive an in-depth map of expression of transcription factors in photoreceptors—potential key players in cell-fate decisions. Third, we explore CRISPR-FØ screening as a fast, efficient and versatile technique to assess the involvement of candidate transcription factors in photoreceptor subtype-specification. We first show that known phenotypes can be easily replicated: loss of S cones in foxq2 mutants and loss of rods in nr2e3 mutants. We then explore four additional transcription factors of unknown function (Skor1a, Sall1a, Lrrfip1a and Xbp1) and find no evidence for their involvement in photoreceptor-subtype specification. Finally, we identify novel functions of Tbx2, demonstrating that it plays a central role in controlling the identity of all photoreceptor sub-types within the retina. Our study provides an open roadmap to discover additional factors involved in this process. This dataset and screening method will be a valuable way to explore the genes involved in many essential aspects of photoreceptor biology.