HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine

As an embryo matures into a fetus, cells undergo remarkable transitions, accompanied by shifts in transcription factor regulatory networks and chromatin landscapes. The mechanisms of these developmental transitions are not completely understood. The embryonic intestine transitions from a rapidly proliferating tube with pseudostratified epithelium prior to embryonic day (E) 14.5, to an exquisitely folded columnar epithelium in the fetus. We sought to define factors that drive fetal maturation of the intestine. ATAC-seq profiling revealed a dramatic restructuring of intestinal chromatin during the embryonic-to-fetal transition, with CDX2 transcription factor motifs abundant at chromatin-accessible regions of the embryo, and hepatocyte nuclear factor 4 (HNF4) transcription factor motifs the most abundant in the fetal stages. Genetic inactivation of Hnf4α and its paralog, Hnf4γ, revealed that HNF4 factors are redundantly and vitally required for fetal maturation. In the embryo, CDX2 binds to and activates Hnf4 gene loci to drive HNF4 expression at fetal stages. HNF4 and CDX2 transcription factors then occupy shared genomic regulatory sites and are required for chromatin accessibility at genes expressed in the maturing fetal intestine. Thus, intestinal transcription factor regulatory networks shift to accompany changing chromatin landscapes and gene expression profiles that occur during the transition of an embryonic tissue to its mature state.