Multiple Roles for the Ess1 Prolyl Isomerase in the RNA Polymerase II Transcription Cycle

Abstract

The Ess1 prolyl isomerase in Saccharomyces cerevisiae regulates RNA polymerase II (pol II) by isomerizing peptide bonds within the pol II carboxy-terminal domain (CTD) heptapeptide repeat (YSPTSPS). Ess1 preferentially targets the Ser5-Pro6 bond when Ser5 is phosphorylated. Conformational changes in the CTD induced by Ess1 control the recruitment of essential cofactors to the pol II complex and may facilitate the ordered transition between initiation, elongation, termination, and RNA processing. Here, we show that Ess1 associates with the phospho-Ser5 form of polymerase in vivo, is present along the entire length of coding genes, and is critical for regulating the phosphorylation of Ser7 within the CTD. In addition, Ess1 represses the initiation of cryptic unstable transcripts (CUTs) and is required for efficient termination of mRNA transcription. Analysis using strains lacking nonsense-mediated decay suggests that as many as half of all yeast genes depend on Ess1 for efficient termination. Finally, we show that Ess1 is required for trimethylation of histone H3 lysine 4 (H3K4). Thus, Ess1 has direct effects on RNA polymerase transcription by controlling cofactor binding via conformationally induced changes in the CTD and indirect effects by influencing chromatin modification.

ACKNOWLEDGMENTS

We are grateful to David Brow, Joan Curcio, Steve Buratowski, Brian Dichtl, Dirk Eick, Mike Hampsey, Caroline Kane, Ian Willis, and Anthony Weil for plasmids, strains, or antibodies, to the Wadsworth Center Molecular Genetics and Media facilities, and to Dave Amberg, Randy Morse, Navjot Singh, and Joe Wade for helpful discussions. We thank Taylor Moon (SUNY—Upstate Summer Undergraduate Fellow) for pilot qRT-PCR experiments and April Burch (Wadsworth Center) for Pin1 experiments.

S.D.H. dedicates this paper to the memory of his mother, Helen Hanes, who first introduced him to research at the famed Bell Telephone Laboratories in Murray Hill, NJ.

This work was funded by grants to S.D.H. from the NIH (grants 3R01-GM055108 and ARRA-GM055108-S1), the NSF (grant MCB-0613001), and SUNY—Upstate Medical University.