mA and the NEXT complex direct Xist RNA turnover and X-inactivation dynamics.

X-chromosome inactivation (XCI) in mammals is orchestrated by the noncoding RNA X-inactive-specific transcript (Xist) that, together with specific interacting proteins, functions in cis to silence an entire X chromosome. Defined sites on Xist RNA carry the N-methyladenosine (mA) modification and perturbation of the mA writer complex has been found to abrogate Xist-mediated gene silencing. However, the relative contribution of mA and its mechanism of action remain unclear. Here we investigate the role of mA in XCI by applying rapid degron-mediated depletion of METTL3, the catalytic subunit of the mA writer complex, an approach that minimizes indirect effects because of transcriptome-wide depletion of mA. We find that acute loss of METTL3 and mA accelerates Xist-mediated gene silencing and this correlates with increased levels and stability of Xist transcripts. We show that Xist RNA turnover is mediated by the nuclear exosome targeting complex but is independent of the principal nuclear mA reader protein YTHDC1. Our findings demonstrate that the primary function of mA on Xist RNA is to promote Xist RNA turnover, which in turn regulates XCI dynamics.