Jonathan P. Staley
Title | Professor |
---|
Institution | University of Chicago |
---|
Department | Molecular Genetics and Cell Biology |
---|
Address | Chicago IL 60637
|
---|
Email |  |
---|
vCard | Download vCard |
---|
|
|
|
Overview 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.
Biography Haverford College, Haverford, PA | B.A. | 1987 | Chemistry | Massachusetts Institute of Technology (Advisor: Peter S. Kim), Boston, MA | Ph.D. | 1993 | Chemistry/Biophysics | University of California at San Francisco, San Francisco, CA | Postdoc | 1999 | Biochemistry/Genetics |
2000 - 2001 | Young Investigator Award, Cancer Research Foundation | 2001 - 2006 | David & Lucile Packard Fellowship in Science and Engineering, Packard Foundation | 2006 - 2008 | Stephen F. Sener, M.D. - Research Scholar Award, American Cancer Society | 2014 | Distinguished Investigator Award, Biological Sciences Division, The University of Chicago | 2016 | Fellow, American Association for the Advancement of Science |
ORNG Applications Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
Faculty can login to make corrections and additions.
-
Zeng Y, Fair BJ, Zeng H, Krishnamohan A, Hou Y, Hall JM, Ruthenburg AJ, Li YI, Staley JP. Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing. Mol Cell. 2022 12 15; 82(24):4681-4699.e8. PMID: 36435176.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
Li NS, Tuttle N, Staley JP, Piccirilli JA. Synthesis and incorporation of the phosphoramidite derivative of 2'-O-photocaged 3'-s-thioguanosine into oligoribonucleotides: substrate for probing the mechanism of RNA catalysis. J Org Chem. 2014 Apr 18; 79(8):3647-52. PMID: 24635216.
-
Wlodaver AM, Staley JP. The DExD/H-box ATPase Prp2p destabilizes and proofreads the catalytic RNA core of the spliceosome. RNA. 2014 Mar; 20(3):282-94. PMID: 24442613.
-
Fica SM, Tuttle N, Novak T, Li NS, Lu J, Koodathingal P, Dai Q, Staley JP, Piccirilli JA. RNA catalyses nuclear pre-mRNA splicing. Nature. 2013 Nov 14; 503(7475):229-34. PMID: 24196718.
-
Koodathingal P, Staley JP. Splicing fidelity: DEAD/H-box ATPases as molecular clocks. RNA Biol. 2013 Jul; 10(7):1073-9. PMID: 23770752.
-
Schellenberg MJ, Wu T, Ritchie DB, Fica S, Staley JP, Atta KA, LaPointe P, MacMillan AM. A conformational switch in PRP8 mediates metal ion coordination that promotes pre-mRNA exon ligation. Nat Struct Mol Biol. 2013 Jun; 20(6):728-34. PMID: 23686287.
-
Kannan R, Hartnett S, Voelker RB, Berglund JA, Staley JP, Baumann P. Intronic sequence elements impede exon ligation and trigger a discard pathway that yields functional telomerase RNA in fission yeast. Genes Dev. 2013 Mar 15; 27(6):627-38. PMID: 23468430.
-
Nielsen KH, Staley JP. Spliceosome activation: U4 is the path, stem I is the goal, and Prp8 is the keeper. Let's cheer for the ATPase Brr2! Genes Dev. 2012 Nov 15; 26(22):2461-7. PMID: 23154979.
-
Semlow DR, Staley JP. Staying on message: ensuring fidelity in pre-mRNA splicing. Trends Biochem Sci. 2012 Jul; 37(7):263-73. PMID: 22564363.
-
Kim Guisbert KS, Zhang Y, Flatow J, Hurtado S, Staley JP, Lin S, Sontheimer EJ. Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae. RNA. 2012 Jun; 18(6):1142-53. PMID: 22539527.
-
Koodathingal P, Novak T, Piccirilli JA, Staley JP. The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5' splice site cleavage during pre-mRNA splicing. Mol Cell. 2010 Aug 13; 39(3):385-95. PMID: 20705241.
-
Mayas RM, Maita H, Semlow DR, Staley JP. Spliceosome discards intermediates via the DEAH box ATPase Prp43p. Proc Natl Acad Sci U S A. 2010 Jun 01; 107(22):10020-5. PMID: 20463285.
-
Zhao C, Bellur DL, Lu S, Zhao F, Grassi MA, Bowne SJ, Sullivan LS, Daiger SP, Chen LJ, Pang CP, Zhao K, Staley JP, Larsson C. Autosomal-dominant retinitis pigmentosa caused by a mutation in SNRNP200, a gene required for unwinding of U4/U6 snRNAs. Am J Hum Genet. 2009 Nov; 85(5):617-27. PMID: 19878916.
-
Mefford MA, Staley JP. Evidence that U2/U6 helix I promotes both catalytic steps of pre-mRNA splicing and rearranges in between these steps. RNA. 2009 Jul; 15(7):1386-97. PMID: 19458033.
-
Staley JP, Woolford JL. Assembly of ribosomes and spliceosomes: complex ribonucleoprotein machines. Curr Opin Cell Biol. 2009 Feb; 21(1):109-18. PMID: 19167202.
-
Anderson AM, Staley JP. Long-distance splicing. Proc Natl Acad Sci U S A. 2008 May 13; 105(19):6793-4. PMID: 18474864.
-
Bellare P, Small EC, Huang X, Wohlschlegel JA, Staley JP, Sontheimer EJ. A role for ubiquitin in the spliceosome assembly pathway. Nat Struct Mol Biol. 2008 May; 15(5):444-51. PMID: 18425143.
-
Hilliker AK, Mefford MA, Staley JP. U2 toggles iteratively between the stem IIa and stem IIc conformations to promote pre-mRNA splicing. Genes Dev. 2007 Apr 01; 21(7):821-34. PMID: 17403782.
-
Mayas RM, Staley JP. DEAD on. Nat Struct Mol Biol. 2006 Nov; 13(11):954-5. PMID: 17082789.
-
Small EC, Leggett SR, Winans AA, Staley JP. The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase. Mol Cell. 2006 Aug 04; 23(3):389-99. PMID: 16885028.
-
Mayas RM, Maita H, Staley JP. Exon ligation is proofread by the DExD/H-box ATPase Prp22p. Nat Struct Mol Biol. 2006 Jun; 13(6):482-90. PMID: 16680161.
-
Leeds NB, Small EC, Hiley SL, Hughes TR, Staley JP. The splicing factor Prp43p, a DEAH box ATPase, functions in ribosome biogenesis. Mol Cell Biol. 2006 Jan; 26(2):513-22. PMID: 16382143.
-
Hilliker AK, Staley JP. Multiple functions for the invariant AGC triad of U6 snRNA. RNA. 2004 Jun; 10(6):921-8. PMID: 15146076.
-
Staley JP. Hanging on to the branch. Nat Struct Biol. 2002 Jan; 9(1):5-7. PMID: 11753425.
-
Chen JY, Stands L, Staley JP, Jackups RR, Latus LJ, Chang TH. Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor. Mol Cell. 2001 Jan; 7(1):227-32. PMID: 11172727.
-
Blank KR, Whittington R, Arjomandy B, Wein AJ, Broderick G, Staley J, Malkowicz SB. Neoadjuvant androgen deprivation prior to transperineal prostate brachytherapy: smaller volumes, less morbidity. Cancer J Sci Am. 1999 Nov-Dec; 5(6):370-3. PMID: 10606479.
-
Staley JP, Guthrie C. An RNA switch at the 5' splice site requires ATP and the DEAD box protein Prp28p. Mol Cell. 1999 Jan; 3(1):55-64. PMID: 10024879.
-
Staley JP, Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell. 1998 Feb 06; 92(3):315-26. PMID: 9476892.
-
Staley JP, Kim PS. Formation of a native-like subdomain in a partially folded intermediate of bovine pancreatic trypsin inhibitor. Protein Sci. 1994 Oct; 3(10):1822-32. PMID: 7531529.
-
Staley JP, Kim PS. Complete folding of bovine pancreatic trypsin inhibitor with only a single disulfide bond. Proc Natl Acad Sci U S A. 1992 Mar 01; 89(5):1519-23. PMID: 1371875.
-
Staley JP, Kim PS. Role of a subdomain in the folding of bovine pancreatic trypsin inhibitor. Nature. 1990 Apr 12; 344(6267):685-8. PMID: 1691452.
This graph shows the total number of publications by year, by first, middle/unknown, or last author.
To see the data from this visualization as text, click here.
Year | Publications |
---|
1990 | 1 | 1992 | 1 | 1994 | 1 | 1998 | 1 | 1999 | 2 | 2001 | 1 | 2002 | 1 | 2004 | 1 | 2006 | 4 | 2007 | 1 | 2008 | 2 | 2009 | 3 | 2010 | 2 | 2012 | 3 | 2013 | 4 | 2014 | 3 | 2015 | 2 | 2016 | 5 | 2017 | 1 | 2019 | 1 | 2022 | 1 |
To return to the timeline, click here.
|
Staley's Networks
Click the "See All" links for more information and interactive visualizations!
Concepts  Derived automatically from this person's publications. _
Co-Authors  People in Profiles who have published with this person. _
Similar People  People who share similar concepts with this person. _
Same Department
People who are also in this person's primary department.
Physical Neighbors  People whose addresses are nearby this person. _
|