3D genome landscaping of in vitro totipotent cellular models [CUT&Tag]
Totipotent embryos lack higher-order genome architecture. In this study, we profile the 3D genome architecture of two putative totipotent cellular models, ciTotiSCs and TBLCs. Notably, both ciTotiSCs and TBLCs retain TADs and structurally resemble ICM/ESCs more closely than totipotent embryos. While TADs and compartmentalization are positionally conserved, they weaken upon acquisition of totipotency. Integrative analysis of epigenetic and Hi-C data further reveal that pluripotency genes undergo coordinated epigenetic landscape remodeling and contact domain reorganization, driving pluripotency suppression. Conversely, totipotency gene activation appears to operate through distinct, yet undefined mechanisms. This study establishes the first functional link between 3D genome folding and totipotency-pluripotency transitions while proposing a revised framework for evaluating in vitro totipotency models. Overall design: CUT&Tag libraries targeting CTCF, H3K27ac, H3K4me3, H3K27me3 and H3K9me3 were prepared from the ESC and the two mouse 2C-like cell lines generated from it, the ciTotiSCs and the TBLCs.