Highly cooperative chimeric super-SOX induces naïve pluripotency across species [ChIP-Seq]
Our understanding of pluripotency remains limited: iPSC generation has only been established for a few model species, pluripotent stem cell lines exhibit inconsistent developmental potential, and germline transmission demonstrated only for mice and rats.  By swapping structural elements between Sox2 and Sox17, we built a chimeric super-SOX factor, Sox2-17, that enhanced iPSC generation in five tested species: mouse, human, cynomolgus monkey, cow, and pig. A swap of alanine to valine at the interface between Sox2 and Oct4 delivered a remarkable gain-of-function by stabilizing Sox2/Oct4 dimerization on DNA, enabling generation of high-grade OSKM iPSCs capable of supporting the development of healthy all-iPSC mice.  Sox2/Oct4 dimerization emerged as the core driver of naïve pluripotency with its levels diminished upon priming. Transient overexpression of Sox2-17 and Klf4 (S*K cocktail) restored the dimerization and boosted the developmental potential of pluripotent stem cells across species, providing a universal method for naïve reset in mammals. Overall design: We performed chromatin immunoprecipitation with sequencing (ChIP-seq) to identify genome-wide binding sites early in reprogramming—48 hours after doxycycline induction of KS2 or KS2AV (Addgene #136617, containing Klf4 and Sox2 or Sox2AV) with or without addition of Oct4 or Oct6 (Addgene #136617 and 136611, O4KS  and O6KS cocktails) in Rosa26rtTA-Gof18 mouse embryonic fibroblasts (MEFs).