Expression status transition of NOTCH1 accompanies chromatin remodeling in human early retinal progenitor cells [version 6; peer review: 1 approved, 3 approved with reservations]

Background Notch signaling, especially via the Notch1 receptor, supports normal eye development by maintaining the retinal progenitor cell state before differentiation, although the regulatory mechanism behind fine-tuned Notch1 expression remains unclear. Methods We re-analyzed publicly available human fetal retina single-cell RNA/ATAC-seq data at days 59, 74, and 78, using Seurat/Signac pipelines. Results We observed NOTCH1 expression in retinal progenitor cells, which diminished later in differentiation. Integration of single-cell RNA-seq and ATAC-seq revealed decreased chromatin accessibility at the NOTCH1 locus, accompanied by decreased mRNA expression, during differentiation into bipolar cells, horizontal cells, or retinal ganglion cells. Importantly, the chromatin remodeling regions contained a binding motif for the RAX transcription factor, which is essential for retinal progenitor cells, Muller glia, and cones. This result suggested that chromatin remodeling at the NOTCH1 locus might regulate NOTCH1 expression, although single-cell RNA-seq analysis suggested that RAX expression regulation might also contribute to NOTCH1 expression. Conclusions By integrating single-cell RNA-seq and ATAC-seq data, this study identified a chromatin remodeling region containing a putative RAX-binding site in the NOTCH1 locus, suggesting that NOTCH1 expression is regulated at both the transcription factor and chromatin levels during early human retinal development.