Onecut1 and Otx2 directly regulate multiple genes expressed early in cone and horizontal cell development [scRNA-seq]
The development of the retina into a highly organized structure occurs via the production of over 100 cell types from a pool of retinal progenitor cells (RPCs). While some RPCs are capable of making many types of retinal cell types, some terminally dividing RPCs are restricted to the production of specific types of daughter cells. Notably, although such restrictions can be limited to the production of a very specific single cell type, in other cases, production of two very different cell types, such as a photoreceptor and an interneuron, occurs. How specific types of RPCs make specific types of neuron is not fully understood. Combining RNA-seq and ATAC-seq, we compared the transcriptome and chromatin profiles between one type of biased RPC and other types of  RPCs. The biased RPC that was studied is one that we previously defined by its expression of a cis-regulatory module (CRM) for the thyroid hormone receptor beta gene (Thrb), the earliest known marker of cone photoreceptors. In this earlier study, we found that Otx2 and Onecut1 drove expression of this Thrb CRM, as well as regulated expression of the Thrb gene. Here we explored the roles of these Otx2 and Oc1 further. We discovered that their roles extend well beyond regulating Thrb. They collaborate to regulate multiple genes important in cone development and/or function, including Rxrg, a known partner of Thrb. We also identified several new enhancers of genes active in developing cones. These data expand our understanding of the gene regulatory network (GRN) for cone development and contribute new CRMs for vectors that are expressed only in cones, as well as enable the genesis of cones from stem cells, for their use in retinal disease cell and gene therapies. Overall design: RNA-seq for ThrbPos and ThrbNeg cells in chick