ATAC-seq analyses of developmental EpCAM+ intestinal epithelial cells

To identify potential cell signaling pathways regulating the proliferative transition of Bmi1+ ISCs from highly proliferative to slow cycling, and also to identify influence for lineage differentiation, we performed bulk ATAC-Seq analyses of FACS-isolated EpCAM+ intestinal cells across developmental time points. Using differential chromatin accessibility analysis we identified enrichment of multiple pathways in the E12.5 population that progressively decreased at E17.5. We analyzed the dataset using identification of motif discovery within this dataset, we found enhanced utilization of transcription factors in pathways including the Hippo signaling pathway (Tead1, Tead2 and Tead4), a known pathway that regulates organ development and size. When we evaluated enrichment motifs for canonical Wnt-responsive loci, we identified occupancy peaking at E14.5, again consistent with transition of proliferative dependency on Bmi1+ to Lgr5+ ISCs. Global motif enrichment for Wnt-related targets was assessed using ChromVAR, which displayed a similar trend, with the canonical Wnt pathway signature peaking at E14.5 and E15.5 (e.g. Cdx2, Tcf4). Epithelial cells from E12.5, E15.5 and E17.5 were isolated from the intestine and processed for ATAC-seq analyses.