Capping enzymes bind the phosphorylated pol II CTD permitting cotranscriptional capping of nascent pre-mRNAs. We asked whether these interactions influence pol II function using ChIP in ts mutants of yeast capping enzymes. Pol II occupancy at the 5' ends of PGK1, ENO2, GAL1, and GAL10 was reduced by inactivation of the methyltransferase, Abd1, but not the guanylyltransferase, Ceg1, suggesting that Abd1 contributes to stable promoter binding. At other genes, Abd1 inactivation increased the 5':3' ratio of pol II density in the promoter-proximal region and caused Ser5 hyperphosphorylation of the pol II CTD. These results suggest an additional role for Abd1 in the promoter clearance and/or promoter-proximal elongation steps of transcription. The transcriptional functions of Abd1 are independent of methyltransferase activity. Manipulation of transcription by Abd1 may enhance cotranscriptional capping and also act as a checkpoint to ensure that a nascent transcript has a cap before it can be completed.