RNA-seq and scRNA-seq reveal trajectory progression of the retinal ganglion cell lineage in wild-type and Atoh7-null retinas

Abstract

Past studies concluded that Atoh7 is critical for the emergence of the retinal ganglion cell (RGC) lineage in the developing retina, whereas Pou4f2 and Isl1 function in RGC differentiation. Atoh7 is expressed in a subset of retinal progenitor cells (RPCs) and is considered a competence factor for the RGC fate, but the molecular properties of these RPCs have not been well characterized. In this study, we first used conventional RNA-seq to investigate transcriptomic changes in Atoh7-, Pou4f2-, and Isl1-null retinas at embryonic (E) day 14.5 and identified the differentially expressed genes (DEGs), which expanded our understanding of the scope of downstream events. We then performed single cell RNA-seq (scRNA-seq) on E13.5 and E17.5 wild-type and Atoh7-null retinal cells. Clustering analysis not only correctly identified known cell types at these developmental stages but also revealed a transitional cell state which was marked by Atoh7 and genes for other lineages in a highly overlapping fashion and shared by all early developmental trajectories. Further, analysis of the Atoh7-null retina revealed that, unlike previously believed, the RGC lineage still progressed considerably and a substantial amount of RGC-specific gene expression still occurred. Thus, Atoh7 likely collaborates with other factors to shepherd the transitional RPCs to the RGC lineage by competing with other lineage factors and activating RGC-specific genes. This study thus provides significant insights into the nature of RPC competence for different retinal cell fates and revises our current view on the emergence of the RGC lineage.