Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [4C-Seq]

To model and characterize the chromatin regulatory landscape of the very first developmental cell fates, we made use of three previously derived and well-characterized Trophoblast Stem Cell (TSCs), Embryonic Stem Cell (ESC) and Extra Embryonic Stem Cell lines (XENs) We performed high-resolution in situ 4C-seq analysis around enhancers and promoters of cell-type specific genes (e.g. Sox17 for XEN and Nanog for ESC), which showed high concordance both with the virtual 4C of HiChIP and the called HiChIP contacts in the respective cell type Overall design: 4C-seq in duplicates / triplicates was performed for selected genes in ESC, TSC and XEN