Integrative Single-cell Transcriptomics and Single-cell Epigenomics Mapping the Developmental Dynamics of Fetal Retina

The underlying mechanisms that determine gene expression and chromatin accessibility in retinogenesis are poorly understood. Here, we performed scRNA-seq and scATAC-seq on human embryonic retina samples from 9 to 26 post-conceptional weeks, explored the heterogeneity of retinal progenitor cells (RPCs) and neurogenic RPCs (NPCs), and verified the differentiation trajectory from RPCs to seven major types of retinal cells. Additionally, we identified cell-lineage-determining transcription factors (TFs) and refined their gene regulatory networks (GRNs) at transcriptomic and epigenomic levels. The inhibitor of RE-1 silencing transcription factor (REST) on retinospheres was found to have led to more neurogenesis with regular arrangement, whereas a decrease of Müller glial cells was observed. We also described the classification of developing RPC-derived cells and their correlation with pathogenic genes of multiple ocular diseases. Overall, we provided a framework for integrated exploration of the developmental dynamics of the human primary retina at the single-cell resolution. We conducted both scRNA-seq and scATAC-seq on developing human embryonic eyes at 9 time points (9, 10, 11, 14, 15, 18, 20, 23, 26) from post-conceptional weeks (PCW) 9 to 26. Therein, PCW26 fetal retina was separated into neuroretina and others two parts. Separate runs of scATAC-seq were performed at PCW11 (one biological replicate) and PCW19. After the initial data processing and quality control, we collected 74,571 single-cell transcriptomes with a median of 2277 genes per cell, and 75,197 single-cell epigenomes with a median of 7604 peak fragments per cell. The matrices obtained were further analyzed using Signac/Seurat (Hao et al., 2021), Chromvar (Schep et al., 2017) and Monocle (Cao et al., 2019; Trapnell et al., 2014).