Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNA Biogenesis

N6-methyladenosine (m6A) regulates various aspects of RNA biology. Although m6A methylation on mRNA has been shown to be co-transcriptionally deposited, a possible regulatory role of m6A on transcription remains poorly understood. Here, we demonstrate that the METTL3/METTL14/WTAP m6A methyltransferase complex (MTC) components are co-localized to many promoters and enhancers and deposit the m6A modification to local chromatin associated transcripts including pre-mRNAs, promoter upstream transcripts (PROMPTs) and enhancer RNAs (eRNAs), suggesting a possible regulatory role for m6A methylation at these transcripts. Indeed, PRO-seq analyses demonstrate that nascent RNAs originating from both promoters and enhancers are significantly decreased in the METTL3 depleted cells. The Integrator complex has been reported to cleave nascent RNAs, which causes transcriptional attenuation. Importantly, simultaneous depletion of METTL3 and INTS11, the endonuclease subunit in the Integrator complex, suppressed the nascent RNA decrease, suggesting an antagonistic relationship between METTL3 and the Integrator complex. Consistently, we found an elevated level of INTS11 at promoters and enhancers upon loss of MTC or the m6A binder HnRNP G. Taken together, our findings suggest that MTC-mediated m6A modification protects nascent RNAs and promotes productive transcription, thus unraveling a novel layer of gene regulation imposed by RNA m6A modification. Overall design: Precision run-on sequencing (PRO-seq) was performed on 6 samples in Drosophila S2 cells. These samples consist of 3 replicates of control (ß-galactosidase targeting dsRNA) and 3 replicates of IntS9 depleted cells.