Dierks David, Shachar Ran, Nir Ronit, Garcia-Campos Miguel Angel, Uzonyi Anna, Wiener David, Toth Ursula, Rossmanith Walter, Lasman Lior, Slobodin Boris, Hanna Jacob H, Antebi Yaron, Scherz-Shouval Ruth, Schwartz Schraga
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
Center for Environmental Genomics, University of Washington, Seattle, United States.
Elife. 2025 Jun 30;13:RP100448. doi: 10.7554/eLife.100448.
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.
N6-甲基腺嘌呤（m6A）是最广泛存在的mRNA修饰，主要参与调控mRNA的稳定性。与m6A相关的基本问题包括其在细胞内以及不同刺激条件下动态调节的程度，以及这种调节背后的机制。先前的研究主要集中在探究调控m6A水平的主动机制，例如招募m6A的写入器或擦除器从而导致“全局”或“位点特异性”的调节。在此，我们提出跨亚细胞区室和生物学轨迹的m6A水平变化可能源于基因水平的mRNA代谢的被动变化。为了预测m6A水平、mRNA定位和mRNA降解之间复杂的相互依赖关系，我们建立了一个差异模型“m6ADyn”，该模型涵盖了mRNA转录、甲基化、输出以及m6A依赖性和非依赖性降解。我们在细胞内m6A动态变化的背景下验证了m6ADyn的预测，其中m6ADyn预测了相对mRNA定位与m6A水平之间的关联，我们通过实验证实了这一点。我们进一步探索了m6ADyn关于mRNA代谢受到控制扰动时m6A水平变化的预测，这也得到了我们实验的证实。最后，我们证明了m6ADyn在细胞热应激反应中的相关性，在这种情况下，mRNA产物和输出发生改变的基因在m6A水平上也表现出可预测的变化，这与m6ADyn的预测一致。我们的研究结果建立了一个剖析m6A动态变化的框架，并揭示了被动动态变化在塑造哺乳动物系统中m6A水平方面的作用。
