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 N-methyladenosine (mA). While depleting mA demethylases represses ATF4 reinitiation, knocking down mA methyltransferases promotes ATF4 translation. We demonstrate that mA 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 mA in translational regulation of ISR at cellular and organismal levels.

Translation acrobatics: how cancer cells exploit alternate modes of translational initiation

“…Recently, m 6 A modifications in the 5′ UTR of the ATF4 mRNA have been discovered. These modifications regulate ATF4 translation by stalling scanning ribosomes on uORF2, thereby reconfiguring translation in response to low ternary complex availability . Although this is a specific, highly characterized example of alternate uORF usage, it illustrates the general principle that uORF usage can change in response to physiological conditions.…”

Altered m6A modification of specific cellular transcripts affects Flaviviridae infection

“…The RIOK3 and CIRBP 225 peaks span four and three DRACH motifs, respectively. Both peaks have been previously 226 reported in published datasets, although the function of m 6 A on these transcripts has not been 227 investigated; the RIOK3 peak was identified in mouse liver tissue (Zhou et al, 2018) MeRIP-RT-qPCR on RNA from cells infected with DENV, ZIKV, and HCV to validate these 230 predicted changes in m 6 A, as in Figure 1F. MeRIP-RT-qPCR confirmed that relative to gene 231 expression, the m 6 A modification of RIOK3 significantly increased following infection and that of 232 CIRBP decreased, while RIOK3 and CIRBP mRNA levels both increased following infection 233 ( Figure 1F Fredericksen, 2010; Suthar et al, 2013).…”

Translational regulation in response to stress in Saccharomyces cerevisiae

“…More recently, other modifications including the methylation of internal adenosine nucleotides to form N 6 -methyladenosine (m 6 A) have emerged as means to regulate mRNA functions such as protein synthesis in a variety of contexts, including in response to stress (Roundtree, Evans, Pan, & He, 2017;Zhou et al, 2018). In yeast, although m 6 A is widespread across different mRNAs, its presence is restricted to meiosis (sporulation), where m 6 A patterns vary over time (Schwartz et al, 2013).…”