Dual states of Bmi1-expressing intestinal stem cells drive epithelial development and tissue regeneration

We demonstrate that Bmi1-expressing cells represent the predominant epithelial ISC in early intestinal development and precede existence of the canonical Wnt-dependent Lgr5+ stem cell population. We reveal that early in development, Bmi1+ ISCs are highly proliferative, then transition to a slow-cycling state with the emergence of the Lgr5+ ISC. Combining single cell RNA-sequencing (scRNA-seq) with bulk population ATAC-seq (Assay for Transposase Accessible Chromatin sequencing) analyses, we identify that a non-canonical Wnt signaling pathway correlates with the temporal presence of the highly proliferative developmental Bmi1+ ISC population. Single Bmi1-expressing murine intestinal epithelial cells were FACS-isolated from embryos at various different ages or adult animals. scRNA-seq was performed using standard protocols.