Nat10 maintains the homeostasis of pluripotent and 2-cell-like states in mouse embryonic stem cells through mRNA cytidine acetylation.

Naïve mouse embryonic stem cells (mESCs) are characterized by a mixed population of cells in an interconvertible pluripotent state and a totipotent 2-cell (2C)-like state. It remains to be understood how the pluripotent state is maintained while the 2C-like state is suppressed. We show that N-acetyltransferase 10 (Nat10) maintains the pluripotent state and suppresses the 2C-like state in mESCs through mRNA modification and stabilization. Nat10 as a nucleolar protein may indirectly interact with heterochromatin through Ncl. Nat10 catalyzes the N4-acetylcytidine (ac4C) modification of mRNAs encoding the key pluripotency genes including Oct4,Esrrb and Zfp42 and enhances their mRNA stability, thus increasing their protein levels for pluripotency. Moreover, Nat10 acetylates and stabilizes heterochromatin modifiers such as Kap1 mRNA and protein to repress the 2C genes by maintaining the H3K9me3 complex. Together, these findings highlight critical roles for Nat10 in maintaining the pluripotency network and repressing the 2C-like program via mRNA ac4C modification, providing insights into the transition between pluripotent and totipotent states in mESCs.