Multi-omics characterization of human Embryonic Stem Cells-derived Pharyngeal Endoderm cells (Histone Modification ChIP-Seq)

We have developed a novel in vitro protocol for the derivation of bona fide Pharyngeal Endoderm (PE) cells from hESCs. We demonstrated that our PE cells robustly express Pharyngeal Endoderm markers, they are transcriptionally similar to PE cells isolated from in vivo mouse development and represent a transcriptionally homogeneous population. Importantly, we elucidated the contribution of Retinoic Acid in promoting a transcriptional and epigenetic rewiring of PE cells. In addition, we defined the epigenetic landscape of PE cells by combining ATAC-Seq and ChIP-Seq of histone marks. We performed ChIP-seq experiments for the histone modifications H4K4me3, H3K4me1, H3K27me3, and H3K27ac on Definitive Endoderm and Pharyngeal endoderm cells (two independent replicates per ChIP experiment) and identified the chromatin states produced by these marks in the two cell types.