The subject of this research project is the structural molecular biology of RNA 3'-end processing and of the integration with transcription and RNA export. RNA processing reactions can be reconstituted in vitro, but they occur more efficiently in the cell because they are closely integrated with transcription. How these biological processes are regulated and integrated with each other remains unclear at the molecular level and poorly understood structurally. Thus, dissecting how transcription and RNA export are coupled with processing at the molecular and structural level, as we propose to do, is an essential step to understanding how gene expression pathways are integrated and regulated. In order to address these biological problems, we propose to study: (1) the molecular basis for the specific recognition of different phosphorylated forms of the C-terminal domain of the RNA polymerase, and how a new phosphatase enzyme generates the form of the CTD found at the 3'-end of genes;(2) the molecular basis for RNA recognition by RNA processing factors in yeast and in vertebrates;(3) the interaction of RNA processing factors with factors that regulate RNA export.

Public Health Relevance

Processing of the 3'-end of RNA by cleavage and polyadenylation is an essential maturation step that is increasingly understood to be critically regulated in cancer and development. Studying structurally and molecularly how it occurs, as we propose, is essential to understanding gene expression and its regulation.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter C
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Washington
Schools of Medicine
United States
Zip Code
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
Sperber, Henrik; Beem, Alan; Shannon, Sandra et al. (2014) miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure. RNA 20:621-31
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
Walbott, Helene; Machado-Pinilla, Rosario; Liger, Dominique et al. (2011) The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic. Genes Dev 25:2398-408
Lunde, Bradley M; Reichow, Steve L; Kim, Minkyu et al. (2010) Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. Nat Struct Mol Biol 17:1195-201
Godin, Katherine S; Walbott, Helene; Leulliot, Nicolas et al. (2009) The box H/ACA snoRNP assembly factor Shq1p is a chaperone protein homologous to Hsp90 cochaperones that binds to the Cbf5p enzyme. J Mol Biol 390:231-44
Deka, Pritilekha; Bucheli, Miriam E; Moore, Claire et al. (2008) Structure of the yeast SR protein Npl3 and Interaction with mRNA 3'-end processing signals. J Mol Biol 375:136-50
Qu, Xiangping; Perez-Canadillas, Jose-Manuel; Agrawal, Shipra et al. (2007) The C-terminal domains of vertebrate CstF-64 and its yeast orthologue Rna15 form a new structure critical for mRNA 3'-end processing. J Biol Chem 282:2101-15
Cho, Hyundae D; Chen, Yu; Varani, Gabriele et al. (2006) A model for C74 addition by CCA-adding enzymes: C74 addition, like C75 and A76 addition, does not involve tRNA translocation. J Biol Chem 281:9801-11
Varani, Gabriele; Chen, Yu; Leeper, Thomas C (2004) NMR studies of protein-nucleic acid interactions. Methods Mol Biol 278:289-312

Showing the most recent 10 out of 11 publications