Proper regulation of RNA Polymerase II (RNAPII) transcription is required for proper gene expression levels and the maintenance of overall genome stability. The regulation of RNAPII is altered in the pathogenesis of many human diseases including cancer, neurological disorders, and viral infection. In order to combat changes in RNAPII transcription during the course of disease progression, the basic mechanisms that underlie the regulation of RNAPII must be understood. We have identified a novel regulator of RNAPII, an atypical protein phosphatase known as Rtr1 that is conserved from yeast to humans. We have shown that Rtr1 is required for dephosphorylation of a specific serine in a conserved domain in RNAPII known as the CTD. However, the mechanisms that require CTD dephosphorylation during transcription are not understood. In order to determine the precise role of Rtr1 during RNAPII transcription, we will focus on three specific questions: (1) Is Rtr1-dependent CTD dephosphorylation required for recruitment of the mRNA 3'end processing machinery? (2) Does Rtr1-dependent dephosphorylation stimulate the release of phospho-CTD binding proteins? and (3) Does Rtr1 regulate the phosphorylation status of other protein complexes involved in the regulation of RNAPII transcription elongation and termination? By addressing these key questions, we will increase our understanding of the fundamental process of RNAPII transcription which will allow us to define how defects in this process cause human disease.

Public Health Relevance

Changes in gene expression and genome stability are hallmarks of human diseases such as cancer. In multiple disease states, changes in gene expression and genome stability and caused by altered regulation of RNAPII gene transcription. Our work will identify novel regulatory mechanisms that are employed during RNAPII transcription that could serve as therapeutic targets for the treatment of human disease.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Sledjeski, Darren D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Indiana University-Purdue University at Indianapolis
Schools of Medicine
United States
Zip Code
Fox, Melanie J; Mosley, Amber L (2016) Rrp6: Integrated roles in nuclear RNA metabolism and transcription termination. Wiley Interdiscip Rev RNA 7:91-104
Bedard, Lynn Glowczewski; Dronamraju, Raghuvar; Kerschner, Jenny L et al. (2016) Quantitative Analysis of Dynamic Protein Interactions during Transcription Reveals a Role for Casein Kinase II in Polymerase-associated Factor (PAF) Complex Phosphorylation and Regulation of Histone H2B Monoubiquitylation. J Biol Chem 291:13410-20
Hunter, Gerald O; Fox, Melanie J; Smith-Kinnaman, Whitney R et al. (2016) Phosphatase Rtr1 Regulates Global Levels of Serine 5 RNA Polymerase II C-Terminal Domain Phosphorylation and Cotranscriptional Histone Methylation. Mol Cell Biol 36:2236-45
Fox, Melanie J; Gao, Hongyu; Smith-Kinnaman, Whitney R et al. (2015) The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway. PLoS Genet 11:e1004999
Hsu, Peter L; Yang, Fan; Smith-Kinnaman, Whitney et al. (2014) Rtr1 is a dual specificity phosphatase that dephosphorylates Tyr1 and Ser5 on the RNA polymerase II CTD. J Mol Biol 426:2970-81
Smith-Kinnaman, Whitney R; Berna, Michael J; Hunter, Gerald O et al. (2014) The interactome of the atypical phosphatase Rtr1 in Saccharomyces cerevisiae. Mol Biosyst 10:1730-41
Ni, Zuyao; Xu, Chao; Guo, Xinghua et al. (2014) RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. Nat Struct Mol Biol 21:686-95
Mosley, Amber L; Hunter, Gerald O; Sardiu, Mihaela E et al. (2013) Quantitative proteomics demonstrates that the RNA polymerase II subunits Rpb4 and Rpb7 dissociate during transcriptional elongation. Mol Cell Proteomics 12:1530-8
Khanna, May; Imasaki, Tsuyoshi; Chikwana, Vimbai M et al. (2013) Expression and purification of functional human glycogen synthase-1 (hGYS1) in insect cells. Protein Expr Purif 90:78-83