Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the crypt/villus transcriptome

The small intestinal epithelium is composed of several defined epithelial cell lineages, which in turn exhibit marked transcriptional and functional diversity along the crypt-villus and proximal-to-distal length of the intestinal tract. While epithelial cell type and functional heterogeneity have been characterized in the adult intestinal epithelium, the temporal and spatial changes during the postnatal period, which accompany the transition from placental energy supply to enteral feeding and facilitate the establishment of the enteric microbiota and postanatal immune maturation, have not been systematically investigated. Here, we analyzed microdissected crypt and villus structures of 1-, 5-, 10-, and 25-day-old SPF mice by 3'mRNA-Seq and used differential gene expression and pathway analysis to identify age-specific expression patterns. We identify gene clusters temporally expressed in the neonatal intestine and correlate their expression with the functional changes during postnatal tissue maturation and the neonate to adult transition. Overall design: To study the difference between crypts and villi, 1 to 2 million µm² of crypts or villi were microdissected from small intestinal tissue obtained from 1-, 5-, 10- and 25-day-old C57Bl/6J specific pathogen-free (SPF) mice using laser-capture microdissection. RNA was then isolated and 3'mRNA-Seq performed.