However, a detailed functional analysis of several metazoan CDKs suggest that Bur1 and its associated cyclin Bur2 are orthologous to the metazoan Cdk9/cyclin T1, while Ctk1 and its cyclin are actually FTY720 orthologs of the metazoan Ctk12/cyclin K. The yeast Bur and Ctk complexes appear to facilitate transcriptional elongation at the 59 and 39 ends of genes, respectively, through a variety of mechanisms including CTD phosphorylation and chromatin modification. The Bur1 kinase is required for efficient elongation by the polymerase and phosphorylates the CTD of RNAPII at Serine 2 near the promoter of genes and at Serine 7. The Bur complex also acts by targeting non-CTD substrates to regulate histone modification and to suppress cryptic transcription. The Ctk complex consisting of the Ctk1 kinase, its associated Ctk2 cyclin, and a third regulatory protein, Ctk3, is also required for elongation by the polymerase, phosphorylates Serine 2 of the CTD, and regulates histone H3 trimethylation. Strong sequence conservation of P-TEFb, Tat-SF1, and the U2 snRNA from mammals to simpler eukaryotes supports the idea that the mechanism whereby P-TEFb and Tat-SF1/U2 snRNA interact to affect elongation may be conserved throughout evolution. To address this possibility, we analyzed the relationship of the homologous factors in yeast. We hypothesized that, if a Bortezomib similar interaction exists in yeast, disruption of either CUS2 or the U2 snRNA would result in the same transcription-related phenotypes exhibited by perturbation of the CDKs. Furthermore, we predicted that these factors would physically associate in a manner similar to their mammalian counterparts. We performed a genetic analysis in Saccharomyces cerevisiae to investigate the in vivo relationship of the CDKs and the U2 snRNP components, Cus2 and U2 snRNA. We find that neither mutating CUS2 nor the U2 snRNA exhibit genetic interactions with the Bur or Ctk complexes. In addition, mutations of the U2 snRNP components do not exhibit phenotypes that have been used previously to assess the roles of P-TEFb homologs in transcription; these phenotypes include sensitivity to 6-azauracil, inositol auxotrophy, and the Spt2 or Bur2 phenotypes. Finally, we were unable to detect physical interactions between these factors. Taken together, we find a lack of evidence for a functional complex containing the yeast CDK complexes and the U2 snRNP. These results suggest that if P-TEFb associates with Tat-SF1 and the U2 snRNA to stimulate transcription in vivo, these interactions are not conserved in yeast. The ability of P-TEFb and Tat-SF1 to physically interact with the U snRNAs, particularly the U2 snRNA was shown to be crucial for the stimulatory effect on transcription. Since Cus2 has been shown to specifically associate with the U2-IIc conformation, we hypothesized that U2 snRNA mutants that preferentially form or disrupt this structure might play a functional role in transcription elongation and that this might be revealed by genetic interactions with the CDKs. To determine whether Bur or Ctk complex function is influenced by a particular conformation of the U2 snRNA, bur2D and ctk2D strains were each crossed with a strain in which the genomic U2 gene was deleted and the U2 snRNA gene was harbored on a plasmid. Mutant U2 snRNA alleles were introduced to the resultant double mutant strains by plasmid shuffling. These previously characterized U2 snRNA plasmids encoded alleles that preferentially form either the U2-IIc or IIa conformation. The U2-IIc allele consists of a G53 to A mutation that favors the U2-IIc conformation by abrogating the formation of the essential IIa stem-loop. The U2- IIa allele hyperstabilizes the essential IIa stem-loop element by deletion of the region of phylogenetically conserved complementarity to stem-loop IIa combined with conversion of the AU stempairs to more thermodynamically stable GC pairs.