The transcriptional coactivator Sub1 has been implicated in several aspects of mRNA metabolism in yeast, such as activation of transcription, termination, and 3-end formation. Here, we present evidence that Sub1 plays a significant role in controlling phosphorylation of the RNA polymerase II large subunit C-terminal domain (CTD). We show that SUB1 genetically interacts with the genes encoding all four known CTD kinases, SRB10, KIN28, BUR1, and CTK1, suggesting that Sub1 acts to influence CTD phosphorylation at more than one step of the transcription cycle. To address this directly, we first used in vitro kinase assays, and we show that, on the one hand, SUB1 deletion increased CTD phosphorylation by Kin28, Bur1, and Ctk1 but, on the other, it decreased CTD phosphorylation by Srb10. Second, chromatin immunoprecipitation assays revealed that SUB1 deletion decreased Srb10 chromatin association on the inducible GAL1 gene but increased Kin28 and Ctk1 chromatin association on actively transcribed genes. Taken together, our data point to multiple roles for Sub1 in the regulation of CTD phosphorylation throughout the transcription cycle.A prominent feature of the largest subunit of RNA polymerase II (RNAP II), Rpb1, is the presence of a highly conserved carboxy-terminal domain (CTD) that has an essential role in transcription regulation in vivo (12,17,54). Although the RNAP II CTD is not required for transcription in promoterindependent assays in vitro, it is essential in vivo (50), and it is required for efficient capping, splicing, and cleavage/polyadenylation of pre-mRNAs (15,29,47). In fact, the CTD has been described as a platform that recruits RNA processing/ export and histone-modifying factors to the transcription complex, coupling mRNA metabolism to chromatin function (8, 54).The CTD is characterized by repetition of the consensus heptapeptide sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser, ranging from 26 repeats in yeast to 52 in mammals, which is subjected to highly regulated phosphorylation (14,15,47). Unphosphorylated RNAP II is mostly recruited to the preinitiation complex (PIC) (45), and hyperphosphorylated RNAP II is associated with initiation and elongation complexes (42). The CTD is phosphorylated on serine 5 of the heptapeptide repeat predominantly during promoter escape and early elongation, while serine 2 becomes phosphorylated principally during elongation (16,38). In addition, it has recently been demonstrated that the CTD can be also phosphorylated on serine 7 (3, 13, 25