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The RNA polymerase II CTD is essential for 3′ end cleavage of metazoan pre-mRNAs and binds 3′ end processing factors in vitro. We show genetic and biochemical interactions between the CTD and the Pcf11 subunit of the yeast cleavage/polyadenylation factor, CFIA. In vitro binding to Pcf11 required phosphorylation of the CTD on Ser2 in the YSPTSPS heptad repeats. Deletion of the yeast CTD reduced the efficiency of cleavage at poly(A) sites, and the length of poly(A) tails suggesting that it helps couple 3′ end formation with transcription. Consistent with this model, the 3′ end processing factors CFIA, CFIB, and PFI were recruited to genes progressively, starting at the 5′ end, in a process that required ongoing transcription.