Structures of co-transcriptional RNA capping enzymes on paused transcription complex

Nascent pre-mRNA undergoes 5' end capping as the first step of processing. Early evidences demonstrated the guanosine addition and 2'-O-ribose methylation spatiotemporally correlated with transcription machinery at the early stage of transcription. Here, we determined cryo-EM structures of PEC (paused elongation complex)-RNGTT (RNA guanylyltransferase and 5' phosphatase) and PEC-RNGTT-CMTR1 (cap-specific mRNA (nucleoside-2'-O-)-methyltransferase). The structures show that RNGTT docks to the root of Pol II stalk through its OB fold. Within RNGTT, the OB fold binds N-terminal of triphosphatase domain and facilitates positioning its catalytic cavity facing towards the RNA exit tunnel. RNGTT dephosphorylates and guanylates PEC-bound RNAs of 17nt, 19nt, 20nt, but not 22nt, in length. CMTR1 arrayed with RNGTT on the Pol II surface through distinct interfaces. Our structures unravel that capping enzymes RNGTT and CMTR1 directly docks to paused elongation complex, and shed light on how pre-mRNA capping couples with Pol II at the specific transcription stage.