Publications

Zhu Y, Wang X, Forouzmand E, Jeong J, Qiao F, Sowd GA, Engelman AN, Xie X, Hertel KJ, Shi, Y, 2018. Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation. Mol Cell. 69(1):62-74.e4. doi: 10.1016/j.molcel.2017.11.031.

Garibaldi A, Carranza F, Hertel KJ, Isolation of Newly Transcribed RNA Using the Metabolic Label 4-Thiouridine. Methods Mol Biol. 2017, 1648:169-176. doi: 10.1007/978-1-4939-7204-3_13.

Movassat M, Shenasa H, Hertel KJ,  Preparation of Splicing Competent Nuclear Extract from Mammalian Cells and In Vitro Pre-mRNA Splicing Assay. Methods Mol Biol.; 2017;1648:11-26. doi: 10.1007/978-1-4939-7204-3_2.

Aubol BE, Wu G, Keshwani MM, Movassat M, Fattet L, Hertel KJ, Fu XD, Adams JA, Release of SR Proteins from CLK1 by SRPK1: A Symbiotic Kinase System for Phosphorylation Control of Pre-mRNA Splicing. Mol. Cell. 2016 Jul 21;63(2):218-228. doi: 10.1016/j.molcel.2016.05.034. Free PMC Article

Movassat M, Crabb TL, Busch A, Yao C, Reynolds DJ, Shi Y, and Hertel, KJ. Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns. RNA Biology. 2016, 7:646-55. doi: 10.1080/15476286.2016.1191727. Free PMC Article

Mueller WF, Larsen LS, Garibaldi A, Hatfield GW, Hertel KJ. The Silent Sway of Splicing by Synonymous Substitutions. J Biol Chem. 2015 Sep 30. pii: jbc.M115.684035. PubMed PMID: 26424794. Free PMC Article

Busch A, Hertel KJ. Splicing predictions reliably classify different types of alternative splicing. RNA. 2015 May;21(5):813-23. doi: 10.1261/rna.048769.114. Epub 2015 Mar 24. PubMed PMID: 25805853; PubMed Central PMCID: PMC4408789. Free PMC Article

Hoverter NP, Zeller MD, McQuade MM, Garibaldi A, Busch A, Selwan EM, Hertel KJ, Baldi P, Waterman ML. The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition. Nucleic Acids Res. 2014 Dec 16;42(22):13615-32. doi: 10.1093/nar/gku1186. Epub 2014 Nov 20. PubMed PMID: 25414359; PubMed Central PMCID: PMC4267635. Free full text

von Figura G, Fukuda A, Roy N, Liku ME, Morris Iv JP, Kim GE, Russ HA, Firpo MA, Mulvihill SJ, Dawson DW, Ferrer J, Mueller WF, Busch A, Hertel KJ, Hebrok M. The chromatin regulator Brg1 suppresses formation of intraductal papillary mucinous neoplasm and pancreatic ductal adenocarcinoma. Nat Cell Biol. 2014 Mar;16(3):255-67. doi: 10.1038/ncb2916. Epub 2014 Feb 23. PubMed PMID: 24561622. Free PMC Article

Morris JP 4th, Greer R, Russ HA, von Figura G, Kim GE, Busch A, Lee J, Hertel KJ, Kim S, McManus M, Hebrok M. Dicer regulates differentiation and viability during mouse pancreatic cancer initiation. PLoS One. 2014 May 1;9(5):e95486. doi: 10.1371/journal.pone.0095486. eCollection 2014. PubMed PMID: 24788257; PubMed Central PMCID: PMC4006805. Free full text

Mueller WF, Hertel KJ. Kinetic analysis of in vitro pre-mRNA splicing in HeLa nuclear extract. Methods Mol Biol. 2014;1126:161-8. doi: 10.1007/978-1-62703-980-2_12. PubMed PMID: 24549663. Free PMC Article

Movassat M, Mueller WF, Hertel KJ. In vitro assay of pre-mRNA splicing in mammalian nuclear extract. Methods Mol Biol. 2014;1126:151-60. doi: 10.1007/978-1-62703-980-2_11. PubMed PMID: 24549662. Free PMC Article

Webb CH, Hertel KJ. Preparation of splicing competent nuclear extracts. Methods Mol Biol. 2014;1126:117-21. doi: 10.1007/978-1-62703-980-2_8. PubMed PMID: 24549659; PubMed Central PMCID: PMC4501576. Free full text

Erkelenz S, Mueller WF, Evans MS, Busch A, Schöneweis K, Hertel KJ, Schaal H. Position-dependent splicing activation and repression by SR and hnRNP proteins rely on common mechanisms. RNA. 2013 Jan;19(1):96-102. doi: 10.1261/rna.037044.112. Epub 2012 Nov 21. Erratum in: RNA. 2013 Jul;19(7):1015. PubMed PMID: 23175589; PubMed Central PMCID: PMC3527730. Free full text

Busch A, Hertel KJ. HEXEvent: a database of Human EXon splicing Events. Nucleic Acids Res. 2013 Jan;41(Database issue):D118-24. doi: 10.1093/nar/gks969. Epub 2012 Oct 31. PubMed PMID: 23118488; PubMed Central PMCID: PMC3531206. Free full text

Busch A, Hertel KJ. Extensive regulation of NAGNAG alternative splicing: new tricks for the spliceosome? Genome Biol. 2012 Feb 22;13(2):143. doi: 10.1186/gb-2012-13-2-143. PubMed PMID: 22356731; PubMed Central PMCID: PMC3334559. Free full text

Busch A, Hertel KJ. Evolution of SR protein and hnRNP splicing regulatory factors. Wiley Interdiscip Rev RNA. 2012 Jan-Feb;3(1):1-12. doi: 10.1002/wrna.100. Epub 2011 Sep 2. Review. PubMed PMID: 21898828; PubMed Central PMCID: PMC3235224. Free full text

Shepard PJ, Choi EA, Busch A, Hertel KJ. Efficient internal exon recognition depends on near equal contributions from the 3′ and 5′ splice sites. Nucleic Acids Res. 2011 Nov 1;39(20):8928-37. doi: 10.1093/nar/gkr481. Epub 2011 Jul 27. PubMed PMID: 21795381; PubMed Central PMCID: PMC3203598. Free full text

Shepard PJ, Choi EA, Lu J, Flanagan LA, Hertel KJ, Shi Y. Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA. 2011 Apr;17(4):761-72. doi: 10.1261/rna.2581711. Epub 2011 Feb 22. PubMed PMID: 21343387; PubMed Central PMCID: PMC3062186. Free full text

Wang E, Mueller WF, Hertel KJ, Cambi F. G Run-mediated recognition of proteolipid protein and DM20 5′ splice sites by U1 small nuclear RNA is regulated by context and proximity to the splice site. J Biol Chem. 2011 Feb 11;286(6):4059-71. doi: 10.1074/jbc.M110.199927. Epub 2010 Dec 2. PubMed PMID: 21127064; PubMed Central PMCID: PMC3039333. Free full text

Han J, Ding JH, Byeon CW, Kim JH, Hertel KJ, Jeong S, Fu XD. SR proteins induce alternative exon skipping through their activities on the flanking constitutive exons. Mol Cell Biol. 2011 Feb;31(4):793-802. doi: 10.1128/MCB.01117-10. Epub 2010 Dec 6. PubMed PMID: 21135118; PubMed Central PMCID: PMC3028638. Free full text

Crabb TL, Lam BJ, Hertel KJ. Retention of spliceosomal components along ligated exons ensures efficient removal of multiple introns. RNA. 2010 Sep;16(9):1786-96. doi: 10.1261/rna.2186510. Epub 2010 Jul 7. PubMed PMID: 20610656; PubMed Central PMCID: PMC2924538. Free full text

Shepard PJ, Hertel KJ. Embracing the complexity of pre-mRNA splicing. Cell Res. 2010 Aug;20(8):866-8. doi: 10.1038/cr.2010.98. Epub 2010 Jul 6. PubMed PMID: 20603640; PubMed Central PMCID: PMC3912182. Free full text

Hicks MJ, Mueller WF, Shepard PJ, Hertel KJ. Competing upstream 5′ splice sites enhance the rate of proximal splicing. Mol Cell Biol. 2010 Apr;30(8):1878-86. doi: 10.1128/MCB.01071-09. Epub 2010 Feb 1. PubMed PMID: 20123971; PubMed Central PMCID: PMC2849477. Free full text

Tannukit S, Crabb TL, Hertel KJ, Wen X, Jans DA, Paine ML. Identification of a novel nuclear localization signal and speckle-targeting sequence of tuftelin-interacting protein 11, a splicing factor involved in spliceosome disassembly. Biochem Biophys Res Commun. 2009 Dec 18;390(3):1044-50. doi: 10.1016/j.bbrc.2009.10.111. Epub 2009 Oct 24. PubMed PMID: 19857462; PubMed Central PMCID: PMC2787706. Free full text

Geib T, Hertel KJ. Restoration of full-length SMN promoted by adenoviral vectors expressing RNA antisense oligonucleotides embedded in U7 snRNAs. PLoS One. 2009 Dec 8;4(12):e8204. doi: 10.1371/journal.pone.0008204. PubMed PMID: 19997596; PubMed Central PMCID: PMC2781471. Free full text

Hsu SN, Hertel KJ. Spliceosomes walk the line: splicing errors and their impact on cellular function. RNA Biol. 2009 Nov-Dec;6(5):526-30. Epub 2009 Nov 18. Review. PubMed PMID: 19829058; PubMed Central PMCID: PMC3912188.Free full text

Klaue Y, Hertel KJ. Dangerous play–splitting the message may leave you empty handed. Nat Struct Mol Biol. 2009 Sep;16(9):907-8. PubMed PMID: 19739289.

Fox-Walsh KL, Hertel KJ. Splice-site pairing is an intrinsically high fidelity process. Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1766-71. doi: 10.1073/pnas.0813128106. Epub 2009 Jan 29. PubMed PMID: 19179398; PubMed Central PMCID: PMC2644112. Free full text

Kotlajich MV, Crabb TL, Hertel KJ. Spliceosome assembly pathways for different types of alternative splicing converge during commitment to splice site pairing in the A complex. Mol Cell Biol. 2009 Feb;29(4):1072-82. doi: 10.1128/MCB.01071-08. Epub 2008 Dec 8. PubMed PMID: 19064642; PubMed Central PMCID: PMC2643811. Free full text

Shepard PJ, Hertel KJ. The SR protein family. Genome Biol. 2009;10(10):242. doi: 10.1186/gb-2009-10-10-242. Epub 2009 Oct 27. Review. PubMed PMID: 19857271; PubMed Central PMCID: PMC2784316. Free full text

Kotlajich MV, Hertel KJ. Death by splicing: tumor suppressor RBM5 freezes splice-site pairing. Mol Cell. 2008 Oct 24;32(2):162-4. doi: 10.1016/j.molcel.2008.10.008. PubMed PMID: 18951082.

Shepard PJ, Hertel KJ. Conserved RNA secondary structures promote alternative splicing. RNA. 2008 Aug;14(8):1463-9. doi: 10.1261/rna.1069408. Epub 2008 Jun 25. PubMed PMID: 18579871; PubMed Central PMCID: PMC2491482. Free full text

Hertel KJ. Combinatorial control of exon recognition. J Biol Chem. 2008 Jan 18;283(3):1211-5. Epub 2007 Nov 16. Review. PubMed PMID: 18024426.

Dou Y, Fox-Walsh KL, Baldi PF, Hertel KJ. Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site. RNA. 2006 Dec;12(12):2047-56. Epub 2006 Oct 19. PubMed PMID: 17053087; PubMed Central PMCID: PMC1664720. Free full text

Hicks MJ, Yang CR, Kotlajich MV, Hertel KJ. Linking splicing to Pol II transcription stabilizes pre-mRNAs and influences splicing patterns. PLoS Biol. 2006 Jun;4(6):e147. Epub 2006 May 2. PubMed PMID: 16640457; PubMed Central PMCID: PMC1450099. Free full text

Sciabica KS, Hertel KJ. The splicing regulators Tra and Tra2 are unusually potent activators of pre-mRNA splicing. Nucleic Acids Res. 2006;34(22):6612-20. Epub 2006 Nov 28. PubMed PMID: 17135210; PubMed Central PMCID: PMC1747189. Free full text

Hicks MJ, Lam BJ, Hertel KJ. Analyzing mechanisms of alternative pre-mRNA splicing using in vitro splicing assays. Methods. 2005 Dec;37(4):306-13. PubMed PMID: 16314259.

Madocsai C, Lim SR, Geib T, Lam BJ, Hertel KJ. Correction of SMN2 Pre-mRNA splicing by antisense U7 small nuclear RNAs. Mol Ther. 2005 Dec;12(6):1013-22. Epub 2005 Oct 14. PubMed PMID: 16226920.

Fox-Walsh KL, Dou Y, Lam BJ, Hung SP, Baldi PF, Hertel KJ. The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16176-81. Epub 2005 Oct 31. PubMed PMID: 16260721; PubMed Central PMCID: PMC1283478. Free full text

Ibrahim EC, Schaal TD, Hertel KJ, Reed R, Maniatis T. Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers. Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):5002-7. Epub 2005 Mar 7. PubMed PMID: 15753297; PubMed Central PMCID: PMC555999. Free full text

Hertel KJ, Graveley BR. RS domains contact the pre-mRNA throughout spliceosome assembly. Trends Biochem Sci. 2005 Mar;30(3):115-8. Review. PubMed PMID: 15752982.

Freund M, Hicks MJ, Konermann C, Otte M, Hertel KJ, Schaal H. Extended base pair complementarity between U1 snRNA and the 5′ splice site does not inhibit splicing in higher eukaryotes, but rather increases 5′ splice site recognition. Nucleic Acids Res. 2005 Sep 9;33(16):5112-9. Print 2005. PubMed PMID: 16155183; PubMed Central PMCID: PMC1201333. Free full text

Lim SR, Hertel KJ. Commitment to splice site pairing coincides with A complex formation. Mol Cell. 2004 Aug 13;15(3):477-83. PubMed PMID: 15304226.

Lam BJ, Bakshi A, Ekinci FY, Webb J, Graveley BR, Hertel KJ. Enhancer-dependent 5′-splice site control of fruitless pre-mRNA splicing. J Biol Chem. 2003 Jun 20;278(25):22740-7. Epub 2003 Mar 19. PubMed PMID: 12646561; PubMed Central PMCID: PMC2386364. Free full text

Lam BJ, Hertel KJ. A general role for splicing enhancers in exon definition. RNA. 2002 Oct;8(10):1233-41. PubMed PMID: 12403462; PubMed Central PMCID: PMC1370333. Free full text

Lim SR, Hertel KJ. Modulation of survival motor neuron pre-mRNA splicing by inhibition of alternative 3′ splice site pairing. J Biol Chem. 2001 Nov 30;276(48):45476-83. Epub 2001 Oct 2. PubMed PMID: 11584013.

Graveley BR, Hertel KJ, Maniatis T. The role of U2AF35 and U2AF65 in enhancer-dependent splicing. RNA. 2001 Jun;7(6):806-18. PubMed PMID: 11421359; PubMed Central PMCID: PMC1370132. Free full text

Hertel KJ, Maniatis T. Serine-arginine (SR)-rich splicing factors have an exon-independent function in pre-mRNA splicing. Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2651-5. PubMed PMID: 10077565; PubMed Central PMCID: PMC15823. Free full text

Graveley BR, Hertel KJ, Maniatis T. SR proteins are ‘locators’ of the RNA splicing machinery. Curr Biol. 1999 Jan 14;9(1):R6-7. PubMed PMID: 9889128.

Hertel KJ, Stage-Zimmermann TK, Ammons G, Uhlenbeck OC. Thermodynamic dissection of the substrate-ribozyme interaction in the hammerhead ribozyme. Biochemistry. 1998 Dec 1;37(48):16983-8. PubMed PMID: 9836592.

Graveley BR, Hertel KJ, Maniatis T. A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers. EMBO J. 1998 Nov 16;17(22):6747-56. PubMed PMID: 9822617; PubMed Central PMCID: PMC1171020. Free full text

Hertel KJ, Maniatis T. The function of multisite splicing enhancers. Mol Cell. 1998 Feb;1(3):449-55. PubMed PMID: 9660929.

Hertel KJ, Peracchi A, Uhlenbeck OC, Herschlag D. Use of intrinsic binding energy for catalysis by an RNA enzyme. Proc Natl Acad Sci U S A. 1997 Aug 5;94(16):8497-502. PubMed PMID: 9238005; PubMed Central PMCID: PMC22973. Free full text

Hertel KJ, Lynch KW, Maniatis T. Common themes in the function of transcription and splicing enhancers. Curr Opin Cell Biol. 1997 Jun;9(3):350-7. Review. PubMed PMID: 9159075.

Hertel KJ, Lynch KW, Hsiao EC, Liu EH, Maniatis T. Structural and functional conservation of the Drosophila doublesex splicing enhancer repeat elements. RNA. 1996 Oct;2(10):969-81. PubMed PMID: 8849774; PubMed Central PMCID: PMC1369430. Free full text

Hertel KJ, Herschlag D, Uhlenbeck OC. Specificity of hammerhead ribozyme cleavage. EMBO J. 1996 Jul 15;15(14):3751-7. PubMed PMID: 8670879; PubMed Central PMCID: PMC452045. Free full text

Stage TK, Hertel KJ, Uhlenbeck OC. Inhibition of the hammerhead ribozyme by neomycin. RNA. 1995 Mar;1(1):95-101. PubMed PMID: 7489494; PubMed Central PMCID: PMC1369065. Free full text

Hertel KJ, Uhlenbeck OC. The internal equilibrium of the hammerhead ribozyme reaction. Biochemistry. 1995 Feb 7;34(5):1744-9. PubMed PMID: 7849034.

Hertel KJ, Herschlag D, Uhlenbeck OC. A kinetic and thermodynamic framework for the hammerhead ribozyme reaction.Biochemistry. 1994 Mar 22;33(11):3374-85. PubMed PMID: 8136375.

Hertel KJ, Pardi A, Uhlenbeck OC, Koizumi M, Ohtsuka E, Uesugi S, Cedergren R, Eckstein F, Gerlach WL, Hodgson R, et al.Numbering system for the hammerhead. Nucleic Acids Res. 1992 Jun 25;20(12):3252. PubMed PMID: 1620624; PubMed Central PMCID: PMC312468. Free full text