N6-Methyladenosine Guides mRNA Alternative Translation during Integrated Stress Response

Abstract

The integrated stress response (ISR) facilitates cellular adaptation to stress conditions via the common target eIF2α. During ISR, the selective translation of stress-related mRNAs often relies on alternative mechanisms, such as leaky scanning or reinitiation, but the underlying mechanism remains incompletely understood. Here we report that, in response to amino acid starvation, the reinitiation of ATF4 is not only governed by the eIF2α signaling pathway, but is also subjected to regulation by mRNA methylation in the form of N⁶-methyladenosine (m⁶A). While depleting m⁶A demethylases represses ATF4 reinitiation, knocking down m⁶A methyltransferases promotes ATF4 translation. We demonstrate that m⁶A in the 5' UTR controls ribosome scanning and subsequent start codon selection. Global profiling of initiating ribosomes reveals widespread alternative translation events influenced by dynamic mRNA methylation. Consistently, Fto transgenic mice manifest enhanced ATF4 expression, highlighting the critical role of m⁶A in translational regulation of ISR at cellular and organismal levels.

Keywords: ATF4; FTO; QTI-seq; alternative translation; epitranscriptome; integrated stress response; m6A; reinitiation; ribosome scanning; start codon selection.