Analysis of gene network branching during optic cup development in zebrafish

Abstract

In all metazoans, sight depends on the intimate relation and combined function of photoreceptors and pigmented cells. These two cell types rise from a pool of common precursors. Unravelling how the gene regulatory networks (GRNs) of these tissues bifurcate into two mutually exclusive developmental programs is an essential step to better understand the molecular basis of retinal degenerative diseases and the branching dynamics of differentiation programs. Here we use the development of the optic cup in zebrafish as a model to explore this biological question, combining RNA-seq and ATAC-seq experiments of different pools of sorted cells derived from distinct domains of the optic cup at several stages of development. This approach allowed us not only to unveil the key specifiers and effector genes operating directly on the morphological and differentiation properties of the eye cells, but also to identify the active cis-regulatory modules orchestrating the specification of its distinct domains. Our results confirm previously known transcription factors as central nodes of the eye GRNs and uncover novel factors playing an unexpected early role in retinal pigmented epithelium (RPE) specification. Further, we untangle how the regulatory dynamics of different transcriptional specifiers harmonize and/or complement each other to carry out the divergent development of the two eye domains. Finally, we tested our findings in human iPSCs differentiating towards RPE cells. This comparison revealed a conserved consecutio temporum of transcription factor recruitment along RPE differentiation program, opening new opportunities for the improvement of therapies for retinal degenerative diseases based on cell replacement. Our work is a further step towards the identification of the molecular links between tissue specifiers and effector molecules involved in eye development, many of which will be causative genes for the most common hereditary malformations of the eye.