Identifying gene regulatory networks controlling photoreceptor specification by transcriptomic and epigenomic analysis of retinal development in cone-dominant retina

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Project Summary While degeneration of cone photoreceptors is the ultimate cause of blindness in photoreceptor dystrophies, mouse and human retinas are rod photoreceptor-dominant, a fact that has hindered progress in understanding how cones are specified. New insight into this problem can potentially come from studying the molecular mechanisms of photoreceptor development in mammalian species with naturally cone-dominant retinas. One such species is the 13-lined ground squirrel (13-LGS) Ictidomys tridecemlineatus, which is endemic to the American Midwest. The genome of 13-LGS is fully sequenced, and their developmental staging is well- characterized and readily comparable to mouse. We propose to comprehensively profile gene expression and chromatin accessibility during retinal neurogenesis in 13-LGS using single-cell RNA- and ATAC-Seq. We will then use computational approaches to identify gene regulatory networks predicted to control cone photoreceptor development in 13-LGS, and compare these with results obtained from mouse and human retinas to identify species-specific differences in gene expression and regulation that underlie differences in the rod:cone ratio. We will also test whether the 13-LGS orthologue of the Nrl gene, a master regulator of photoreceptor specification, shows reduced ability to promote rod, and repress cone, development relative to its mouse counterpart. We expect these studies will identify multiple previously unidentified genes that are strong candidate positive and negative regulators of cone development, and can be functionally tested in future studies. Ultimately, this may help improve protocols for directed differentiation of cone photoreceptors from stem and progenitor cells for use in therapeutic transplantation.