The largest subunit of RNA polymerase II contains a unique C-terminal domain important for coupling of transcription and mRNA processing. This domain consists of a repeated heptameric sequence (YSPTSPS) phosphorylated at serines 2 and 5. Serine 5 is phosphorylated during initiation and recruits capping enzyme. Serine 2 is phosphorylated during elongation by the Ctk1 kinase, a protein similar to mammalian Cdk9/P-TEFb. Chromatin immunoprecipitation was used to map positions of transcription elongation and mRNA processing factors in strains lacking Ctk1. Ctk1 is not required for association of elongation factors with transcribing polymerase. However, in ctk1Δ strains, the recruitment of polyadenylation factors to 3′ regions of genes is disrupted and changes in 3′ ends are seen. Therefore, Serine 2 phosphorylation by Ctk1 recruits factors for cotranscriptional 3′ end processing in vivo.