m⁶A RNA methylation regulates promoter- proximal pausing of RNA polymerase II

Highlights

• m⁶A MTC recruitment to the chromatin regulates pausing of RNAP II

• Mettl3 induces pause release, and this effect depends on its catalytic domain

• m⁶A MTC recruitment can be predicted by RNAP II and pause factor occupancies

• m⁶A MTC interacts with Spt6, and its recruitment is partially dependent on Spt6

Summary

RNA polymerase II (RNAP II) pausing is essential to precisely control gene expression and is critical for development of metazoans. Here, we show that the m⁶A RNA modification regulates promoter-proximal RNAP II pausing in Drosophila cells. The m⁶A methyltransferase complex (MTC) and the nuclear reader Ythdc1 are recruited to gene promoters. Depleting the m⁶A MTC leads to a decrease in RNAP II pause release and in Ser2P occupancy on the gene body and affects nascent RNA transcription. Tethering Mettl3 to a heterologous gene promoter is sufficient to increase RNAP II pause release, an effect that relies on its m⁶A catalytic domain. Collectively, our data reveal an important link between RNAP II pausing and the m⁶A RNA modification, thus adding another layer to m⁶A-mediated gene regulation.