The Staley Lab

the staley lab

splicing research at the university of chicago

About the Staley Lab

In the Staley Lab, we use genetic, biochemical, biophysical, and genome-wide techniques to tease apart the inner workings of the spliceosome: the catalyst for nuclear pre-mRNA splicing.

Long known to be an essential step in eukaryotic gene expression, understanding the mechanism, fidelity, and transcriptome-wide effects of changes in pre-mRNA splicing will deepen our knowledge of the regulation of cellular function and development. 

Splicing Catalysis

Pioneering work by our lab, in collaboration with Joe Piccirilli, shows U6 snRNA coordinates metals to cataylze both transesterification steps of pre-mRNA splicing, further supporting the hypothesis that the spliceosome and the group II self-splicing intron share an evolutionary origin (Fica & Tuttle et al., Nature, 2013).

Mechanisms of DEAH-box Helicase Translocation

Through the combination of x-ray crystallography, yeast genetics, and comparative structure analyses, we have uncovered the importance of several structural motifs in mediating the 3′ to 5′ translocase activity of the model DEAH-box helicase Prp43 (He et al., RNA, 2017).

Genome-Wide Interrogation of Splicing

Using the model organism S. cerevisiae, we developed a method of enriching for and sequencing excised lariat introns, allowing interrogation and discovery of novel branch points and 5′ splice sites (Qin et al., RNA, 2016).

Alternative Splice Site Selection

Alternative splicing is a major form of transcriptome diversity, with upwards of 90% of human genes being alternatively spliced. Our lab discovered both alternative branch site usage and alternative 3′ splice site usage can be mediated by the ATP-dependent activities of the DEAH-box helicases Prp16 and Prp22 (Semlow et al., Cell, 2016).

Fidelity of Splicing

As an essential part of gene expression, splicing has to proceed with high fidelity. Work from our lab shows DEAH-box helicases in the spliceosome work to proofread several steps in the splicing process (Semlow & Staley, TiBS, 2012), from Prp2 proofreading the catalytic core  (Wlodaver & Staley, RNA, 2014), to Prp16 and Prp43 cooperating to discard spliceosomes stalled 5′ splice site cleavage (Koodathingal et al., Mol Cell, 2010), to Prp22 proofreading the exon ligation stage of splicing (Mayas et al., NSMB, 2006).

Our Team

Jon Staley

Jon Staley

Principal Investigator

Klaus Nielsen

Klaus Nielsen

Senior Research Professional

Yi Zeng, PhD

Yi Zeng, PhD

Postdoctoral Researcher

James Hagerty, PhD

James Hagerty, PhD

Postdoctoral Researcher

Yichen Hou

Yichen Hou

Graduate Student, Genetics Genomics and Systems Biology

Chris Craddock

Chris Craddock

Graduate Student, Cell and Molecular Biology

Astra Hwang

Astra Hwang

Graduate Student, Genetics Genomics and Systems Biology

Cody Hernandez

Cody Hernandez

Graduate Student, Cell and Molecular Biology

Matthew McDonough

Matthew McDonough

Graduate Student, Cell and Molecular Biology

Zhongshi Wang

Zhongshi Wang

Graduate Student, Cell and Molecular Biology

Lab Alumni

Aiswarya Krishnamohan, PhD

Scientist at Skyhawk Therapeutics

Rebecca Toroney, PhD

Senior Scientist at Abbott

Daoming Qin, PhD

Senior Data Analyst at Capital One

Daniel Semlow, PhD

Assistant Professor at Caltech

Sebastian Fica, PhD

Sir Henry Dale Fellow at Oxford University

Deepti Bellur, PhD

Freelance Proofreader at Medjaden Bioscience Limited

Alissa Wlodaver, PhD MLS(ASCP)

Genome Analyst at Lurie Children's Hospital

Prakash Koodathingal, PhD

Expert Scientist at GSK

Melissa Mefford, PhD

Assistant Professor at Morehead State University

Rabiah Mayas, PhD

Associate Director, Science in Society at Northwestern

Eliza Small, PhD

Scientist at Thermo Fisher Scientific

Angie Hilliker, PhD

Associate Professor at The University of Richmond

Hiroshi Maita, PhD

Senior Lecturer at Hokkaido University

Nina Leeds, PhD

SVP, Medical Director at VMLY&R

Cristian Camacho

Chef, Osito's Tap


Retsch Ball Mill Protocol by the Staley Lab



Profiling of Nascent Lariat Intermediates Reveals Key Genetic Determinants of the Timing of Human Co-transcriptional Splicing
Zeng, Y., Fair F.J., Krishanamohan, A., Hou, Y., Hall, J.M., Ruthenburg, A.J., and Staley, J.P.
bioRxiv 2021, pre-print.

Termination of pre-mRNA splicing requires that the ATPase and RNA unwindase Prp43 acts on the catalytic snRNA U6 
Toroney, R., Nielsen K.H., and Staley, J.P.
Genes Dev 2019, 33(21-22):1555-1574.

Termination of pre-mRNA splicing requires that the ATPase and RNA unwindase Prp43 acts on the catalytic snRNA U6 
Toroney, R., Nielsen K.H., and Staley, J.P.
bioRxiv 2019, pre-print

Structure of DEAH/RHA ATPase Prp43p bound to RNA implicates a pair of hairpins and motif Va in translocation along RNA
He Y., Staley J.P., Andersen G.R., and Nielsen K.H.
RNA 2017, 23(7)1110-1124.

Reverse transcriptases lend a hand in splicing catalysis
Piccirilli, J.A. and Staley, J.P.
Nat Struct Molec Biol 2016, 23(6): 507-9.

Spliceosomal DEAH-box ATPases remodel pre-mRNA to activate alternative splice sites
Semlow, D.R., Blanco, M.R., Walter, N.G., and Staley, J.P.
Cell 2016, 164(5): 985-98.

Sequencing of lariat termini in S. cerevisiae reveals 5′ splice sites, branch points, and novel splicing events
Qin, D.Q., Huang, L., Wlodaver, A.M., Andrade, J., and Staley, J.P.
RNA 2016, 22(2): 237-53.

Evidence for formation of a catalytic triplex in the spliceosome
Fica, S.M.†, Mefford, M.A.†, Piccirilli, J.A., and Staley, J.P. †Co-first authors.
Nat Struct Mol Biol 2014, 21: 464-71.

The DExD/H-box ATPase Prp2p destabilizes and proofreads the catalytic RNA core of the spliceosome
Wlodaver, A.M., and Staley, J.P.
RNA 2013, 20: 1-13.

RNA catalyzes nuclear pre-mRNA splicing
†Fica, S.M., †Tuttle, N., Novak, T., Li, N.S., Lu, J., Koodathingal, P., Dai, Q., Staley, J.P., and Piccirilli, J.A. †Co-first authors.
Nature 2013, 503: 229-234.

Mechanistic Insights into Mammalian pre-mRNA splicing
Fica, S.M., Small, E.C., Mefford, M., Staley, J.P.
2013, In Post-transcriptional Gene Regulation: RNA Processing in Eukaryotes, J.Y. Wu, ed.
Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, pp. 133–161

Splicing fidelity: DEAD/H-box ATPases as molecular clocks
Koodathingal, P., and Staley, J.P.
RNA Biol 2013, 10: 1073-1079.

A conformational switch in PRP8 mediates metal ion coordination that promotes pre-mRNA exon ligation
Schellenberg, M.J., Ritchie, D.B., Fica, S.M., Staley, J.P., Atta, K.A., LaPointe, P., MacMillan, A.M.
Nat Struct Mol Biol 2013, 20:728-734.

Intronic sequence elements impede exon ligation and trigger a discard pathway that yields funcional telomerase RNA in fission yeast
Kannan, R., Hartnett, S., Voelker, R.B., Berglund, J.A., Staley J.P., and Baumann, P.
Genes Dev 2013, 27:627-638.

Spliceosome activation: U4 is the path, stem 1 is the goal, and Prp8 is the keeper. Let’s cheer for the ATPase Brr2!
Nielsen, K.H., and Staley, J.P.
Genes Dev 2012, 22:2461-2467.

Staying on message: ensuring fidelity in pre-mRNA splicing
Semlow, D.R., and Staley, J.P.
Trends in Biochem Sci 2012, 7:263-273.

Meiosis-induced alterations in transcript architecture and noncoding RNA
expression in S. cerevisiae

Kim Guisbert, K.S., Zhang, Y., Flatow, J., Hurtado, S., Staley, J.P., Lin, S., and Sontheimer, E.J.
RNA 2013, 18:1142-1153.

The DEAH Box ATPases Prp16 and Prp43 Cooperate to Proofread 5′ Splice Site Cleavage during Pre-mRNA Splicing
Koodathingal, P., Novak, T., Piccirilli, J.A., and Staley, J.P.
Mol Cell 2010, 39:385-395.

The spliceosome discards intermediates via the DEAH box ATPase Prp43p
Mayas, R.M., Maita, H., Semlow, D.R. and Staley, J.P.
Proc Natl Acad Sci 2010, 107:10020-10025.


Autosomal-Dominant Retinitis Pigmentosa Caused by a Mutation in SNRNP200, a Gene Required for Unwinding of U4/U6 snRNAs
Zhao, C., Bellur, D.L., Lu, S., Zhao, F., Grassi, M.A., Bowne, S.J., Sullivan, L.S., Daiger, S.P., Chen, L.J., Pang, C.P., Zhao, K., Staley, J.P., and Larsson, C.
Am J Hum Genet 2009, 85:617-627.

Evidence that U2/U6 helix I promotes both catalytic steps of pre-mRNA splicing and rearranges in between these steps
Mefford, M A. and Staley, J.P.
RNA 2009, 15:1386-1397.

Assembly of ribosomes and spliceosomes: complex ribonucleoprotein machines
Staley, J.P. and Woolford J.L. Jr.
Curr Opin Cell Biol 2009, 21:109-118.

Long-distance Splicing
Anderson, A.M. and Staley, J.P.
Proc Natl Acad Sci USA 2008, 105:1693-1694.

A Role for Ubiquitin in the Spliceosome Assembly Pathway
Bellare, P., Small, E.C., Huang, X., Wohlschlegel, J.A., Staley, J.P. and Sontheimer, E.J.
Nat Struct Mol Biol 2008, 15(5):444-51.

U2 toggles iteratively between the stem IIa and stem IIc conformations to promote pre-mRNA splicing
Hilliker, A.K., Mefford, M A. and Staley, J.P.
Genes Dev 2007, 21(7):821-834.

Mayas, R.M. and Staley, J.P.
Nat Struct Mol Biol 2006, 13:954-955.

The EF-G-like GTPase Snu114 Regulates Spliceosome Dynamics Mediated by Brr2p, a DExD/H-box ATPase
Small, E.C., Leggett, S.R., Winans, A.A. and Staley, J.P.
Mol Cell 2006, 23(3):389-99.

Exon ligation is proofread by the DExD/H-box ATPase Prp22p
Mayas, R.M., Maita, H. and Staley, J.P.
Nat Struct Mol Biol 2006, 13:482-490.

The splicing factor Prp43p, a DEAH box ATPase, functions in ribosome biogenesis
Leeds, N.B., Small, E.C., Hiley, S.L., Hughes, T.R. and Staley, J.P.
Mol Cell Biol 2006, 26:513-22.

Multiple functions for the invariant AGC triad of U6 snRNA
Hilliker, A.K. and Staley, J.P.
RNA 2004, 10:921-928.

Hanging on to the branch
Staley, J.P.
Nat Struct Biol 2002, 9:5-7.

Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor
Chen, J.Y.F., Stands, L. Staley, J.P., Jackups, R.R., Jr. and Chang, T.H.
Mol Cell 2001, 7:227.


An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. 
Staley, J.P. and Guthrie, C.
Mol Cell 1999, 3:55-64.

Mechanical devices of the spliceosome: motors, clocks, springs and things. 
Staley, J.P. and Guthrie, C.
Cell 1998, 92:315-326.

Formation of a native-like subdomain in a partially folded intermediate of bovine pancreatic trypsin inhibitor
Staley, J.P. and Kim, P.S.
Protein Sci 1994, 3:1822-1832.

Complete folding of bovine pancreatic trypsin inhibitor with only a single disulfide bond 
Staley, J.P. and Kim, P.S.
Proc Natl Acad Sci USA 1992, 89:1519-1523.

Role of a subdomain in the folding of bovine pancreatic trypsin inhibitor 
Staley, J.P. and Kim, P.S.
Nature 1990, 344:685-688

Contact Us

The Staley Lab is housed in Cummings Life Science Center in the UChicago Science Quad, located west of the main campus and east of Comer’s Children Hospital.

Address: 920 East 58th Street, Chicago, IL 60637

Lab: CLSC 817 / (773) 834-5885

Office: CLSC 812A / (773) 834-5886


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