People

Jonathan P. Staley, PhD

Our goal is to understand the mechanism and regulation of nuclear pre-mRNA splicing, an essential step in eukaryotic gene expression. Pre-mRNA splicing is catalyzed by a massive multimegadalton ribonucleoprotein machine called the spliceosome. Using the model organism S. cerevisiae, we apply a wide array of approaches, ranging from single molecule microscopy, biophysics, and chemical biology to biochemistry and cell biology to genetics and genomics to gain a deep understanding of how the spliceosome catalyzes and regulates pre-mRNA splicing.

University of California at San Francisco
San Francisco, CA
Postdoc - Biochemistry/Genetics
1999

Massachusetts Institute of Technology (Advisor: Peter S. Kim)
Boston, MA
Ph.D. - Chemistry/Biophysics
1993

Haverford College
Haverford, PA
B.A. - Chemistry
1987

Termination of pre-mRNA splicing requires that the ATPase and RNA unwindase Prp43p acts on the catalytic snRNA U6.
Toroney R, Nielsen KH, Staley JP. Termination of pre-mRNA splicing requires that the ATPase and RNA unwindase Prp43p acts on the catalytic snRNA U6. Genes Dev. 2019 11 01; 33(21-22):1555-1574.
PMID: 31558568

Structure of the DEAH/RHA ATPase Prp43p bound to RNA implicates a pair of hairpins and motif Va in translocation along RNA.
He Y, Staley JP, Andersen GR, Nielsen KH. Structure of the DEAH/RHA ATPase Prp43p bound to RNA implicates a pair of hairpins and motif Va in translocation along RNA. RNA. 2017 07; 23(7):1110-1124.
PMID: 28416566

Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment.
Shao Y, Huang H, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA, Piccirilli JA. Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment. J Mol Biol. 2016 10 09; 428(20):4100-4114.
PMID: 27593161

The Evolutionarily-conserved Polyadenosine RNA Binding Protein, Nab2, Cooperates with Splicing Machinery to Regulate the Fate of pre-mRNA.
Soucek S, Zeng Y, Bellur DL, Bergkessel M, Morris KJ, Deng Q, Duong D, Seyfried NT, Guthrie C, Staley JP, Fasken MB, Corbett AH. The Evolutionarily-conserved Polyadenosine RNA Binding Protein, Nab2, Cooperates with Splicing Machinery to Regulate the Fate of pre-mRNA. Mol Cell Biol. 2016 11; 36(21):2697-2714.
PMID: 27528618

Reverse transcriptases lend a hand in splicing catalysis.
Piccirilli JA, Staley JP. Reverse transcriptases lend a hand in splicing catalysis. Nat Struct Mol Biol. 2016 06 07; 23(6):507-9.
PMID: 27273636

Cancer therapies activate RIG-I-like receptor pathway through endogenous non-coding RNAs.
Ranoa DR, Parekh AD, Pitroda SP, Huang X, Darga T, Wong AC, Huang L, Andrade J, Staley JP, Satoh T, Akira S, Weichselbaum RR, Khodarev NN. Cancer therapies activate RIG-I-like receptor pathway through endogenous non-coding RNAs. Oncotarget. 2016 May 03; 7(18):26496-515.
PMID: 27034163

Spliceosomal DEAH-Box ATPases Remodel Pre-mRNA to Activate Alternative Splice Sites.
Semlow DR, Blanco MR, Walter NG, Staley JP. Spliceosomal DEAH-Box ATPases Remodel Pre-mRNA to Activate Alternative Splice Sites. Cell. 2016 Feb 25; 164(5):985-98.
PMID: 26919433

Sequencing of lariat termini in S. cerevisiae reveals 5' splice sites, branch points, and novel splicing events.
Qin D, Huang L, Wlodaver A, Andrade J, Staley JP. Sequencing of lariat termini in S. cerevisiae reveals 5' splice sites, branch points, and novel splicing events. RNA. 2016 Feb; 22(2):237-53.
PMID: 26647463

Knocking Down Snrnp200 Initiates Demorphogenesis of Rod Photoreceptors in Zebrafish.
Liu Y, Chen X, Qin B, Zhao K, Zhao Q, Staley JP, Zhao C. Knocking Down Snrnp200 Initiates Demorphogenesis of Rod Photoreceptors in Zebrafish. J Ophthalmol. 2015; 2015:816329.
PMID: 26137319

Evidence for a group II intron-like catalytic triplex in the spliceosome.
Fica SM, Mefford MA, Piccirilli JA, Staley JP. Evidence for a group II intron-like catalytic triplex in the spliceosome. Nat Struct Mol Biol. 2014 May; 21(5):464-471.
PMID: 24747940

View All Publications

Fellow
American Association for the Advancement of Science
2016

Distinguished Investigator Award, Biological Sciences Division
The University of Chicago
2014

Stephen F. Sener, M.D. - Research Scholar Award
American Cancer Society
2006 - 2008

David & Lucile Packard Fellowship in Science and Engineering
Packard Foundation
2001 - 2006

Young Investigator Award
Cancer Research Foundation
2000 - 2001