The Staley Lab

Publications

2010-Present

Export of discarded splicing intermediates requires mRNA export factors and the nuclear basket
Zeng, Y., and Staley, J.P.
eLife 2024

Profiling of Nascent Lariat Intermediates Reveals Key Genetic Determinants of the Timing of Human Co-transcriptional Splicing
Zeng, Y., Fair F.J., Zeng H., Krishanamohan, A., Hou, Y., Hall, J.M., Ruthenburg, A.J., and Staley, J.P.
Molecular Cell 2022

Profiling of Nascent Lariat Intermediates Reveals Key Genetic Determinants of the Timing of Human Co-transcriptional Splicing
Zeng, Y., Fair F.J., Zeng H., 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.

2000-2009

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.

DEAD on
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.

1990-1999

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

 

3 + 7 =