Passive shaping of intra- and intercellular m6A dynamics via mRNA metabolism

Abstract m6A is the most widespread mRNA modification and is primarily implicated in controlling mRNA stability. Fundamental questions pertaining to m6A are the extent to which it is dynamically modulated within cells and across stimuli, and the forces underlying such modulation. Prior work has focused on investigating active mechanisms governing m6A levels, such as recruitment of m6A writers or erasers leading to either ‘global’ or ‘site-specific’ modulation. Here, we propose that changes in m6A levels across subcellular compartments and biological trajectories may result from passive changes in gene-level mRNA metabolism. To predict the intricate interdependencies between m6A levels, mRNA localization, and mRNA decay, we establish a differential model ‘m6ADyn’ encompassing mRNA transcription, methylation, export, and m6A-dependent and independent degradation. We validate the predictions of m6ADyn in the context of intracellular m6A dynamics, where m6ADyn predicts associations between relative mRNA localization and m6A levels, which we experimentally confirm. We further explore m6ADyn predictions pertaining to changes in m6A levels upon controlled perturbations of mRNA metabolism, which we also experimentally confirm. Finally, we demonstrate the relevance of m6ADyn in the context of cellular heat stress response, where genes subjected to altered mRNA product and export also display predictable changes in m6A levels, consistent with m6ADyn predictions. Our findings establish a framework for dissecting m6A dynamics and suggest the role of passive dynamics in shaping m6A levels in mammalian systems. Competing Interest Statement The authors have declared no competing interest. Footnotes ↵6 Lead Contact In this revision, we addressed reviewer feedback by conducting additional experiments and clarifying key aspects of the manuscript. Notably, we performed nuclear-cytoplasmic fractionation experiments on WTAP-depleted cells during a heat shock time course. These results revealed that while m6A levels were reduced, the observed mRNA localization changes persisted, further supporting that m6A is not a primary driver of these shifts and that observed changes in m6A level are rather a result of the changes in mRNA metabolism. Textual changes were made to emphasize the passive regulation of m6A through transcriptional induction and changes in export. Further computational code has been supplied in Supplementary Table 1 allowing an implementation of m6ADyn.