RNA polymerase (RNAP) II catalyzes the transcription of protein-coding genes in eukaryotic cells. The largest subunit of RNAP II contains at its cis C-terminus an unusual domain consisting of multiple repeats of the consensus sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. This C-terminal domain (CTD) is extensively phosphorylated in RNAP IIO and unphosphorylated in RNAP IIA. Each round of transcription appears to be associated with reversible phosphorylation of the CTD. The studies proposed here will provide a critical test of the hypothesis that the CTD functions at multiple steps in the transcription cycle and that its activity is modulated by phosphorylation. This proposal is specifically concerned with an analysis of the CTD of mammalian RNAP II in the hope of better understanding its function and the consequences of the modifications that occur within it. The two primary objectives of this proposal are a) to define the interactions in which the CTD participates as RNAP II progress through the transcription cycle and b) to characterize the protein kinases and protein phosphatases that modulate the state of phosphorylation of the CTD. An understanding of the involvement of the CTD at specific steps in the transcription process is dependent on defining the proteins with which it interacts and how these interactions are influenced by phosphorylation. A novel approach to determining CTD interactions within the context of the transcription apparatus is to modify the CTD with a photoreactive probe and define these contacts by protein-protein crosslinking. CTD interactions with the transcription apparatus will also be defined by identifying transcription factors that mediate the differential interactions of RNAPs IIA and IIO with the preinitiation complex. An understanding of the regulation of CTD kinases and CTD phosphatase(s) that together control the extent of CTD phosphorylation is also fundamental to the understanding of how the activity of RNAP II is regulated. This proposal emphasizes the characterization and molecular cloning of the genes encoding two distinct CTD kinases, designed CTDK1 and CTDK2, that appear to recognize different target sequences within the consensus repeat. An analysis of CTDK1 and CTDK2 in conjunction with the tyrosine CTD kinase c-Abl will provide a test of the idea that phosphorylation of the CTD with different protein kinases can generate distinct conformations that differentially influence RNAP II activity. This proposal is also concerned with the characterization and molecular cloning of the gene(s) encoding a recently purified CTD phosphatase and an examination of how CTD phosphatase activity is regulated.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Molecular Biology Study Section (MBY)
Program Officer
Tompkins, Laurie
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Davis
Schools of Arts and Sciences
United States
Zip Code
Yeo, Michele; Lin, Patrick S (2007) Functional characterization of small CTD phosphatases. Methods Mol Biol 365:335-46
Tremeau-Bravard, Alexandre; Riedl, Thilo; Egly, Jean-Marc et al. (2004) Fate of RNA polymerase II stalled at a cisplatin lesion. J Biol Chem 279:7751-9
Palancade, Benoit; Marshall, Nicholas F; Tremeau-Bravard, Alexandre et al. (2004) Dephosphorylation of RNA polymerase II by CTD-phosphatase FCP1 is inhibited by phospho-CTD associating proteins. J Mol Biol 335:415-24
Yeo, Michele; Lin, Patrick S; Dahmus, Michael E et al. (2003) A novel RNA polymerase II C-terminal domain phosphatase that preferentially dephosphorylates serine 5. J Biol Chem 278:26078-85
Liu, Y V; Clark, D J; Tchernajenko, V et al. (2003) Role of C-terminal domain phosphorylation in RNA polymerase II transcription through the nucleosome. Biopolymers 68:528-38
Lin, Patrick S; Dahmus, Michael E (2003) Dephosphorylation of the carboxyl-terminal domain of RNA polymerase II. Methods Enzymol 370:155-65
Lin, Patrick S; Tremeau-Bravard, Alexandre; Dahmus, Michael E (2003) The repetitive C-terminal domain of RNA polymerase II: multiple conformational states drive the transcription cycle. Chem Rec 3:235-45
Lin, Patrick S; Marshall, Nicholas F; Dahmus, Michael E (2002) CTD phosphatase: role in RNA polymerase II cycling and the regulation of transcript elongation. Prog Nucleic Acid Res Mol Biol 72:333-65
Hawkes, Nicola A; Otero, Gabriel; Winkler, G Sebastiaan et al. (2002) Purification and characterization of the human elongator complex. J Biol Chem 277:3047-52
Lin, Patrick S; Dubois, Marie-Francoise; Dahmus, Michael E (2002) TFIIF-associating carboxyl-terminal domain phosphatase dephosphorylates phosphoserines 2 and 5 of RNA polymerase II. J Biol Chem 277:45949-56

Showing the most recent 10 out of 39 publications