Developmental Competence Encoded at the Level of Enhancers

The emergence of distinct cell types during embryonic development relies on the ability of progenitor cells to properly interpret environmental cues; yet how this developmental competence is established is unknown. Here we show that epigenetic priming of enhancers signifies developmental competence. Chromatin mapping during endodermal lineage diversification of human pluripotent stem cells revealed en masse acquisition of a poised chromatin state at enhancers for multiple descendant lineages in developmental intermediates. The responsiveness of developmental intermediates to lineage-inductive signals is dependent on a poised enhancer state. We further find that lineage-specific enhancers are first recognized by transcription factors involved in chromatin priming, while subsequent recruitment of lineage-inductive transcription factors leads to enhancer and target gene activation. Together, our results identify acquisition of a poised chromatin state at enhancers as a general mechanism by which progenitor cells gain the competence to rapidly activate lineage-specific genes in response to inductive signals. The overall goal of this study was the examine the dynamic changes in the enhancer landscape during endodermal and pancreatic differentiation of hESCs. Specifically we performed ChIP-seq of enhancer related histone modifications (H3K4me1 and H3K27ac) during a five stage differentiation (ES, DE, GT, FG and PE) of hESCs to the pancreatic lineage with two independent biological replicates. To further investigate enhancer activity we performed GRO-seq analysis during the same time course. Additionally, we performed ChIP-seq of the pancreatic regulator PDX1 in hESC derived pancreatic endoderm. To assess its effect on enhancers we also performed H3K27ac ChIP-seq on hESC derived PE transduced with shRNA targeting PDX1 as well as a scrambled control. H3K27ac ChIP-seq was also performed on hESC derived hepatic endoderm using two different protocols to examine enhancer activity during the liver/pancreas lineage decision. Lastly, to investigate the role of pioneer transcription factors at enhancers, we performed ChIP-seq of FOXA1 and FOXA2 during the same five stage pancreatic timecourse.