The C-terminal domain (CTD) of the largest subunit of RNA polymerase II plays critical roles in the initiation, elongation and processing of primary transcripts. These activities are at least partially regulated by the phosphorylation of the CTD by three cyclin-dependent protein kinases (CDKs), namely CDK7, CDK8 and CDK9. In this study, we systematically compared the phosphorylation of different recombinant CTD substrates by recombinant CDK7/ CycH/MAT1, CDK8/CycC and CDK9/CycT1 kinases. We showed that CDK7, CDK8 and CDK9 produce different patterns of phosphorylation of the CTD. CDK7/CycH/ MAT1 generates mostly hyperphosphorylated full-length and truncated CTD peptides, while CDK8/CycC and CDK9/CycT1 generate predominantly hypophosphorylated peptides. Total activity towards different parts of the CTD also differs between the three kinases; however, these differences did not correlate with their ability to hyperphosphorylate the substrates. The last 10 repeats of the CTD can act as a suppressor of the activity of the kinases in the context of longer peptides. Our results indicate that the three kinases possess different biochemical properties that could reflect their actions in vivo.Keywords: carboxy-terminal domain; cyclin-dependent kinase; phosphorylation; RNA pol II.The C-terminus of the largest subunit of the eukaryotic RNA polymerase II consists of multiple repeats of a YSPTSPS consensus heptapeptide sequence [1,2]. This part of the polypeptide is referred to as CTD (C-terminal domain). In higher eukaryotes, the CTD consists of 52 heptapeptide repeats [1][2][3]. The N-terminal portion of the CTD contains mainly perfect YSPTSPS repeats; however, the repeats in the C-terminal portion significantly deviate from the consensus [2-5], probably reflecting a more specialized function of this part of the polypeptide. It has been demonstrated that the N-terminal half of the CTD supports RNA synthesis and capping of the primary transcript [6][7][8], whereas the C-terminal half supports splicing and 3¢ processing of the transcripts [6]. The importance of the C-terminal ISPDDSDEEN sequence of the CTD in the regulation of transcript processing has also been shown [9]. The CTD is phosphorylated at multiple sites, which leads to the production of two forms of RNA polymerase II in vivo: a hypophosphorylated form called IIa, and a hyperphosphorylated form called IIo [1,2,4,5]. It is well established that phosphorylation of the CTD regulates the transition of RNA polymerase II from initiation to elongation, the capping of primary transcripts and the efficiency of pol II elongation [1,2,10]. CTD phosphorylation has also been implicated in the cotranscriptional splicing and polyadenylation of nascent transcripts [1,2,10]. However, little is known about how the phosphorylation of different parts of the CTD contributes to these functions.At least three protein kinases are involved directly in the phosphorylation of the CTD and in the regulation of different stages of mRNA synthesis [1,2]. Cyclin dependent kinase (CDK)7, in conjunct...