3D genome topologies distinguish pluripotent epiblast and primitive endoderm cells in the mouse blastocyst

The development of embryonic cell lineages is tightly controlled by transcription factors that regulate gene expression and chromatin organisation. To investigate the specialisation of 3D genome structure in pluripotent or extra-embryonic endoderm lineages, we applied Genome Architecture Mapping (GAM) in embryonic stem (ES) cells, extra-embryonic endoderm (XEN) stem cells, and in their in vivo counterparts, the epiblast (Epi) and primitive endoderm (PrE) cells, respectively. We discover extensive differences in 3D genome topology including the formation domain boundaries that differ between Epi and PrE lineages, both in vivo and in vitro, at lineage commitment genes. In ES cells, Sox2 contacts other active regions enriched for NANOG and SOX2 binding sites. PrE-specific genes, such as Lama1 and Gata6, form repressive chromatin hubs in ES cells. Lama1 activation in XEN or PrE cells coincides with its extensive decondensation. Putative binding sites for OCT4 and SNAIL, or GATA4/6, distinguish chromatin contacts unique to embryonic or extra-embryonic lineages, respectively. Overall, 3D genome folding is highly specialised in early development, especially at genes encoding factors driving lineage identity. ### Competing Interest Statement AP holds a patent on Genome Architecture Mapping: Pombo, A., Edwards, P. A. W., Nicodemi, M., Scialdone, A., Beagrie, R. A. Patent EP 3,230,465 B1, US 10,526,639 B2 (2015).