A direct interaction between CPF and Pol II links RNA 3ʹ-end processing to transcription

Transcription termination by RNA Polymerase II (Pol II) is linked to RNA 3ʹ-end processing by the cleavage and polyadenylation factor (CPF). CPF contains endonuclease, poly(A) polymerase and protein phosphatase activities that cleave and polyadenylate the pre-mRNA, and dephosphorylate Pol II to control transcription. Exactly how the RNA 3ʹ-end processing machinery is coupled to transcription remains unclear. Here, we combine in vitro reconstitution, electron cryo-microscopy and X-ray crystallography to show that CPF physically and functionally interacts with Pol II. Surprisingly, CPF-mediated dephosphorylation promotes the formation of a Pol II stalk-to-stalk homodimer. This dimer is compatible with transcription (unlike other Pol II dimers) but not with the binding of transcription elongation factors. We show that the Ref2 subunit of CPF contributes directly to the interaction with Pol II and also regulates the Glc7/PP1 CPF phosphatase. We hypothesize that Pol II dimerization may play a role in gene looping and may provide a mechanistic basis for the allosteric model of transcription termination.