Unique activities of two overlapping PAX6 retinal enhancers

Enhancers play a critical role in development by precisely modulating spatial, temporal, and cell type-specific gene expression. Sequence variants in enhancers have been implicated in disease, however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development, with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive, redundant, or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers, HS5 and NRE. Using a unique combination of live imaging and single-cell RNA sequencing in dual enhancer-reporter zebrafish embryos, we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping, these enhancers have distinct activities in different cell types and therefore likely non-redundant functions. This work demonstrates that unique cell type-specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active, we carried out scRNA-seq on eyes from NRE-eGFP/HS5-mCherry zebrafish reporter embryos. With this technique, we aimed to uncover cell type or transcriptional differences between the two enhancer-active populations. We dissected eyes from 48 hpf NRE-eGFP/HS5-mCherry embryos and used FACS to enrich for either mCherry-positive/HS5-active cells or eGFP-positive/NRE-active cells. Three samples for each population were processed for scRNA-seq using the 10x Genomics Chromium single cell 3' gene expression technology.