Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell [ATAC-Seq]

Enterocytes and four classic secretory cell types derive from intestinal epithelial stem cells. Based on morphology, location, and canonical markers, goblet and Paneth cells are considered distinct secretory types. Here, we report high overlap in their transcripts and sites of accessible chromatin, in marked contrast to those of their enteroendocrine or tuft cell siblings. Mouse and human goblet and Paneth cells express extraordinary fractions of few antimicrobial genes, which reflect specific responses to local niches. Wnt signaling retains some ATOH1+ secretory cells in crypt bottoms, where absence of BMP signaling potently induces Paneth features. Cells that migrate away from crypt bottoms encounter BMPs and thereby acquire goblet properties. These phenotypes and underlying accessible cis-elements interconvert in post-mitotic cells. Thus, goblet and Paneth properties represent alternative phenotypic manifestations of a common signal-responsive terminal cell type. These findings reveal exquisite niche-dependent cell plasticity and cis-regulatory dynamics in likely response to antimicrobial needs. Overall design: Mouse duodenal organoids were treated with DAPT for 3 days, then continued for additional 4 days with DAPT and with WnthiBMPlo or Wntlo BMPhi conditions along with DAPT, and cells were collected for bulk ATAC-seq. Lgr5 GFP+ ISC or villi enterocytes from VilCreER-T2;Apcfl/fl mice 3 weeks after tamoxifen induction IP (1mg/ml) were harvested for bulkATAC-seq.