Distinct Processes and Transcriptional Targets Underlie CDX2 Requirements in Intestinal Stem Cells and Differentiated Villus Cells

Lgr5-expressing intestinal stem cells (ISCs) renew the adult gut epithelium by producing mature villus cells (VCs); the transcriptional basis for ISC functions remains unclear. RNA sequencing analysis identified transcripts modulated during differentiation of Lgr5+ ISCs into VCs, with high expression of the intestine-restricted transcription factor (TF) gene Cdx2 in both populations. Cdx2-deleted mouse ISCs showed impaired proliferation and long-term inability to produce mature lineages, revealing essential ISC functions. Chromatin immunoprecipitation sequencing analysis of CDX2 in Lgr5+ ISCs, coupled with mRNA profiling of control and Cdx2−/− ISCs, identified features of CDX2 regulation distinct from VCs. Most CDX2 binding in ISCs occurs in anticipation of future gene expression, but whereas CDX2 primarily activates VC genes, direct ISC targets are activated and repressed. Diverse CDX2 requirements in stem and differentiated cells may reflect the versatility of TFs that specify a tissue in development and control the same tissue in adults. [Display omitted] •The TF Cdx2 is highly expressed in intestinal stem cells and villus cells•CDX2 is required for proliferation and differentiation of intestinal stem cells•CDX2 binding in stem cells anticipates future villus cell gene expression•Direct CDX2 targets in ISCs may be activated or repressed Shivdasani and colleagues demonstrate an essential role for transcription factor CDX2 in replication and differentiation of intestinal stem cells (ISCs). Considering CDX2 binding together with transcriptional changes during epithelial differentiation, they show that binding in ISCs anticipates future gene expression. Through analysis of Cdx2-null ISCs, they identify direct target genes, which are activated or repressed and may underlie the defects.