Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation

Abstract

During development, all retinal cell types emerge from multipotent retinal progenitor cells (RPCs) following distinct trajectories. Each lineage is subject to regulation by multiple intrinsic and extrinsic factors, which converge onto the epigenetic landscape to dictate the collective gene expression profile and thereby the phenotypes of individual cell states/types. Recent scRNA-seq studies have further delineated these trajectories, providing a general picture of the relationships between the different cell states/types and revealing a transitional RPC state shared by all the early lineages. Nevertheless, how the epigenetic landscape shifts along individual trajectories is only beginning to be disseminated, and the roles of key transcription factors in these shifts are not known. In this study, we dissect the changes of the epigenetic landscape along these trajectories in the early developing retina by scATAC-seq and identify globally the enhancers, enriched motifs, and potential interacting transcription factors underlying the cell state/type specific gene expression in individual lineages, with a focus on retinal ganglion cells (RGCs). Using CUT&Tag-seq, we further identify the enhancers bound directly by four key transcription factors, Otx2, Atoh7, Pou4f2, and Isl1, and uncover their roles in shaping the epigenetic landscape to control gene expression in a sequential and combinatorial fashion during RGC genesis. These results provide experimental support for a general paradigm in which transcription factors collaborate and compete to regulate the emergence of distinct retinal cell types such as RGCs from the multipotent transitional RPCs.