Transcription by RNA polymerase II (pol II) requires the ordered binding of 
distinct protein complexes to catalyze initiation, elongation, termination, and 
coupled mRNA processing events. One or more proteins from each complex are known 
to bind pol II via the carboxy-terminal domain (CTD) of the largest subunit, 
Rpb1. How binding is coordinated is not known, but it might involve 
conformational changes in the CTD induced by the Ess1 peptidyl-prolyl cis/trans 
isomerase. Here, we examined the role of ESS1 in transcription by studying one 
of its multicopy suppressors, BYE1. We found that Bye1 is a negative regulator 
of transcription elongation. This led to the finding that Ess1 also inhibits 
elongation; Ess1 opposes elongation factors Dst1 and Spt4/5, and overexpression 
of ESS1 makes cells more sensitive to the elongation inhibitor 6-AU. In reporter 
gene assays, ess1 mutations reduce the ability of elongation-arrest sites to 
stall polymerase. We also show that Ess1 acts positively in transcription 
termination, independent of its role in elongation. We propose that Ess1-induced 
conformational changes attenuate pol II elongation and help coordinate the 
ordered assembly of protein complexes on the CTD. In this way, Ess1 might 
regulate the transition between multiple steps of transcription.