Small Molecule-Inducible and Photoactivatable Cellular RNA N1-Methyladenosine Editing.

N1-methyladenosine (mA) modification is one of the most prevalent epigenetic modifications on RNA. Given the vital role of mA modification in RNA processing such as splicing, stability and translation, developing a precise and controllable mA editing tool is pivotal for in-depth investigating the biological functions of mA. In this study, we developed an abscisic acid (ABA)-inducible and reversible mA demethylation tool (termed AI-dmA), which targets specific transcripts by combining the chemical proximity-induction techniques with the CRISPR/dCas13b system and ALKBH3. We successfully employed AI-dmA to selectively demethylate the mA modifications at A8422 of MALAT1 RNA, and this demethylation process could be reversed by removing ABA. Furthermore, we validated its demethylation function on various types of cellular RNAs including mRNA, rRNA and lncRNA. Additionally, we used AI-dmA to specifically demethylate mA on ATP5D mRNA, which promoted ATP5D expression and enhanced the glycolysis activity of tumor cells. Conversely, by replacing the demethylase ALKBH3 with methyltransferase TRMT61A, we also developed a controllable mA methylation tool, namely AI-mA. Finally, we caged ABA by 4,5-dimethoxy-2-nitrobenzyl (DMNB) to achieve light-inducible mA methylation or demethylation on specific transcripts. Collectively, our mA editing tool enables us to flexibly study how mA modifications on specific transcript influence biological functions and phenotypes.