ABSTRACT

Pancreatic islets control glucose homeostasis primarily through beta cells, whose loss or dysfunction underlies diabetes. Diabetics could be cured through transplantation of new beta cells generated in vitro, but this has been limited by an incomplete understanding of the mechanisms driving their specification and functional maturation. To better understand these mechanisms, we exploited the stepwise differentiation of beta cells from human stem cells and devised methods to purify lineage intermediates, which enabled global DNA methylation, chromatin accessibility, and histone modification profiling. We thus elucidate the landscape of regulatory domains, the pioneer factors that establish them, and their dynamics throughout human beta cell development. We find that endocrine specification involves de novo establishment of enhancer repertoires and is foreshadowed by priming of lineage-specifying loci. Accordingly, we identify polyhormonal cells as alpha cell progenitors by showing that priming of alpha cell-specific enhancers steers them toward an alpha-cell fate in vivo. We further define core regulatory circuits for each pancreatic developmental stage by dissecting autoregulatory loops formed by super-enhancer-driven transcription factors. These include both known and unexpected regulators such as LMX1B, which we validate as critical for endocrine differentiation. Finally, by contrasting epigenomes of maturing stem derived beta cells with their in vivo counterparts, we uncover a role for circadian rhythms in eliciting mature glucose responsiveness. Metabolically synchronized beta cells show rhythmic expression of genes controlling insulin release and rhythmic insulin secretion with an increased glucose threshold, a hallmark of functional maturity. These findings reveal mechanisms orchestrating human islet cell specification and maturation.