Expression status transition of NOTCH1 accompanies chromatin remodeling in human early retinal progenitor cells

<ns7:p> Background The regulation of receptor expression is crucial for fine-tuned signal transduction. Notch signaling is a key signaling pathway involved in retinal development. Compared to the knowledge on this signaling pathway in the differentiation of retinal ganglion cells, less is known about its involvement in earlier stages of retinal progenitor cell differentiation and its regulation, although <ns7:italic>NOTCH1,</ns7:italic> and probably <ns7:italic>NOTCH3,</ns7:italic> are involved in earlier stage differentiation. We aimed to clarify the timing of Notch receptor expression in undifferentiated retinal progenitor cells and elucidate the possible involvement of chromatin remodeling in the regulation of Notch receptor expressions. Methods We re-analyzed publicly available human fetal retina single-cell RNA-seq and ATAC-seq data (GSE183684) using Seurat/Signac pipelines. Results On days 59, 74 and 78, we observed <ns7:italic>NOTCH1</ns7:italic> and <ns7:italic>NOTCH3</ns7:italic> mRNA expressions in early retinal progenitor cells, which diminished at later stages of differentiation. Integration of single-cell RNA-seq and ATAC-seq revealed that chromatin remodeling in part of the <ns7:italic>NOTCH1</ns7:italic> and <ns7:italic>NOTCH3</ns7:italic> loci were accompanied by transitions in their mRNA expressions. Importantly, the <ns7:italic>NOTCH1</ns7:italic> locus, which showed chromatin remodeling, contained multiple binding motifs for transcription factors important in early retinal progenitor cell differentiation. Since genome-wide investigation of transcription factor binding motifs showed enrichment of such motifs for the early retinal progenitor cell-associated transcription factors (LHX2, RAX and VSX2), the motifs in the <ns7:italic>NOTCH1</ns7:italic> locus might be of biological significance rather than observed by chance. Indeed, footprinting analysis suggested actual binding of those transcription factors (LHX2, RAX and VSX2) and their motifs in the whole genome, strengthening potential involvement of these transcription factor activities in early retinal progenitor cell differentiation. Conclusions These results suggest that chromatin remodeling may be involved in the differential expression of <ns7:italic>NOTCH1</ns7:italic> , although another type of Notch mRNA expression regulations may also exist. </ns7:p>