Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin [GLORI]
Interaction between the m6A methyltransferase METTL3 and METTL14 is critical for METTL3 to deposit m6A on various types of RNAs. It is still intriguing whether there is spatial control of m6A deposition on different types of RNAs. Here, through genome-wide CRISPR/Cas9 screening based on a bimolecular fluorescence complementation (BIFC) reporter, we find the H3K27ac acetylase p300 and PAK2 inhibit the interaction between METTL3 and METTL14. We further find that p300-catalyzed acetylation of METTL3 specifically occurs on H3K27ac marked chromatin. METTL3 acetylation suppresses the binding of METTL3 on H3K27ac-marked chromatin by inhibiting its interaction with METTL14. Disruptive K-to-R mutations on the three METTL3 acetylation sites promote the m6A of chromatin-associated RNAs transcribed from p300 bound enhancers and promoters marked by H3K27ac and H3K4me1-3 other than those regions marked by H3K36me3 and H3K9me3, resulting in degradation of eRNAs and paRNAs and transcription inhibition of ferroptosis-inhibition related genes. In addition, PAK2 promotes METTL3 acetylation by phosphorylating METTL3. Inhibition of PAK2 promotes the ferroptosis induced by RSL3, ML162, as well as the chemotherapy drug CDDP in a manner that depends on the acetylation of METTL3. Our study reveals a spatial-selective way to specifically regulate the deposition of m6A on enhancer and promoter RNAs. Overall design: Chromatin-associated RNA m6A profiles of METTL3-WT or METTL3-3KR A549 cells were generated by deep sequencing, in diplicate, using SURFSeq 5000 platform on PE100 mode.