Defining context-dependent m6A RNA methylomes in Arabidopsis

N⁶-Methyladenosine (m⁶A) prevalently occurs on cellular RNA across almost all kingdoms of life. It governs RNA fate and is essential for development and stress responses. However, the dynamic, context-dependent m⁶A methylomes across tissues and in response to various stimuli remain largely unknown in multicellular organisms. Here, we generate a comprehensive census that identifies m⁶A methylomes in 100 samples during development or following exposure to various external conditions in Arabidopsis thaliana. We demonstrate that m⁶A is a suitable biomarker to reflect the developmental lineage, and that various stimuli rapidly affect m⁶A methylomes that constitute the regulatory network required for an effective response to the stimuli. Integrative analyses of the census and its correlation with m⁶A regulators identify multiple layers of regulation on highly context-dependent m⁶A modification in response to diverse developmental and environmental stimuli, providing insights into m⁶A modification dynamics in the myriad contexts of multicellular organisms.