The Regulatory Logic of Planarian Stem Cell Differentiation [scRNAseq]

Stem cell differentiation underlies development and regeneration in multicellular organisms. Cell type identity is determined by the expression of specific transcription factors (TFs) regulating target genes (TGs) via binding to open chromatin regions (OCRs). The regulatory logic of differentiation includes factors specific to one or multiple cell types, functioning in a combinatorial fashion. Single cell transcriptomics has emerged as a revolutionary approach to study gene expression with cell type resolution, but integrating it with single cell analysis techniques to study chromatin remains challenging. Planarians, with their pluripotent neoblast stem cells continuously giving rise to all cell types, offer an ideal model to attempt this integration. Despite extensive single cell transcriptomic studies, the transcriptional and chromatin regulation at the cell type level remains unexplored. Here, we investigate the regulatory logic of planarian stem cell differentiation by obtaining an organism-level integration of single cell transcriptomics and single cell ATAC-seq. We identify specific open chromatin profiles for major differentiated cell types and analyse their transcriptomic landscape, revealing distinct gene modules expressed in individual types and combinations of them. Integrated analysis unveils gene networks reflecting known TF interactions in each type and identifies TFs potentially driving differentiation across multiple cell types. To validate our predictions, we combined TF knockdown RNAi experiments with single cell transcriptomics. We focus on hnf4, a TF known to be expressed in gut phagocytes, and confirm its influence on other types, including parenchymal cells. Our results demonstrate high overlap between predicted targets and experimentally-validated differentially-regulated genes. Overall, our study integrates TFs, TGs and OCRs to reveal the regulatory logic of planarian stem cell differentiation, showcasing the potential of single cell methods for characterising differentiation trajectories and their regulation. Overall design: Four SPLiT-Seq RNA-Seq libraries of ACME-dissociated whole Schmidtea mediterranea animals in unperturbed conditions and two SPLiT-Seq RNA-Seq libraries of ACME-dissociated whole S. mediterranea animals in gfpi and hnf4i knock-down conditions.