NAT10‐mediated ac⁴C modification promotes ectoderm differentiation of human embryonic stem cells via acetylating NR2F1 mRNA

Abstract

Cell fate determination in mammalian development is complex and precisely controlled and accumulating evidence indicates that epigenetic mechanisms are crucially involved. N4‐acetylcytidine (ac4C) is a recently identified modification of messenger RNA (mRNA); however, its functions are still elusive in mammalian. Here, we show that N‐acetyltransferase 10 (NAT10)‐mediated ac4C modification promotes ectoderm differentiation of human embryonic stem cells (hESCs) by acetylating nuclear receptor subfamily 2 group F member 1 (NR2F1) mRNA to enhance translation efficiency (TE). Acetylated RNA immunoprecipitation sequencing (acRIP‐seq) revealed that levels of ac4C modification were higher in ectodermal neuroepithelial progenitor (NEP) cells than in hESCs or mesoendoderm cells. In addition, integrated analysis of acRIP‐seq and ribosome profiling sequencing revealed that NAT10 catalysed ac4C modification to improve TE in NEP cells. RIP‐qRT‐PCR analysis identified an interaction between NAT10 and NR2F1 mRNA in NEP cells and NR2F1 accelerated the nucleus‐to‐cytoplasm translocation of yes‐associated protein 1, which contributed to ectodermal differentiation of hESCs. Collectively, these findings point out the novel regulatory role of ac4C modification in the early ectodermal differentiation of hESCs and will provide a new strategy for the treatment of neuroectodermal defects diseases.

ac4C: a fragile modification with stabilizing functions in RNA metabolism

“…ac4C RIP-seq has proven invaluable in various cellular studies, confirming ac4C's presence in mRNA and aiding in uncovering its functional roles in diverse pathways including cellular proliferation, cellular development, the DNA damage response, and innate immunity ( Ge et al 2023 ; Jiang et al 2023 ; Liu et al 2023a ; Shi et al 2023 ; Wang et al 2023 ; Xie et al 2023 ). However, this method has its limitations.…”

“…These unexpected results suggest that NAT10's critical cellular functions are related to other substrates, including perhaps mRNA. Indeed, the mRNA substrates of NAT10 have been linked to multiple essential pathways including cellular proliferation and differentiation ( Arango et al 2018 ; Fei et al 2021 ; Ge et al 2023 ; Jiang et al 2023 ; Liu et al 2023a ). How NAT10 is dynamically regulated to reach the correct mRNA substrates at the correct time is an underexplored area of ac4C research, though variations in NAT10 levels during development and in response to specific stimuli are emerging as contributing factors.…”