My Bibliography

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Ruden DM, Ma J, Li Y, Wood K, Ptashne M. Generating yeast transcriptional activators containing no yeast protein sequences. Nature. 1991 Mar 21;350(6315):250-2. doi: 10.1038/350250a0. PubMed PMID: 2005981.

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Sadowski I, Niedbala D, Wood K, Ptashne M. GAL4 is phosphorylated as a consequence of transcriptional activation. Proc Natl Acad Sci U S A. 1991 Dec 1;88(23):10510-4. doi: 10.1073/pnas.88.23.10510. PubMed PMID: 1961715; PubMed Central PMCID: PMC52958.

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Lynch KW, Maniatis T. Synergistic interactions between two distinct elements of a regulated splicing enhancer. Genes Dev. 1995 Feb 1;9(3):284-93. doi: 10.1101/gad.9.3.284. PubMed PMID: 7867927.

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Lynch KW, Maniatis T. Assembly of specific SR protein complexes on distinct regulatory elements of the Drosophila doublesex splicing enhancer. Genes Dev. 1996 Aug 15;10(16):2089-101. doi: 10.1101/gad.10.16.2089. PubMed PMID: 8769651.

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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.

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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. doi: 10.1016/s0955-0674(97)80007-5. Review. PubMed PMID: 9159075.

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Lynch KW, Weiss A. A model system for activation-induced alternative splicing of CD45 pre-mRNA in T cells implicates protein kinase C and Ras. Mol Cell Biol. 2000 Jan;20(1):70-80. doi: 10.1128/MCB.20.1.70-80.2000. PubMed PMID: 10594010; PubMed Central PMCID: PMC85051.

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Lynch KW, Weiss A. A CD45 polymorphism associated with multiple sclerosis disrupts an exonic splicing silencer. J Biol Chem. 2001 Jun 29;276(26):24341-7. doi: 10.1074/jbc.M102175200. Epub 2001 Apr 16. PubMed PMID: 11306584.

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Sheives P, Lynch KW. Identification of cells deficient in signaling-induced alternative splicing by use of somatic cell genetics. RNA. 2002 Dec;8(12):1473-81. PubMed PMID: 12515380; PubMed Central PMCID: PMC1370353.

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Rothrock C, Cannon B, Hahm B, Lynch KW. A conserved signal-responsive sequence mediates activation-induced alternative splicing of CD45. Mol Cell. 2003 Nov;12(5):1317-24. doi: 10.1016/s1097-2765(03)00434-9. PubMed PMID: 14636588.

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Lynch KW. Consequences of regulated pre-mRNA splicing in the immune system. Nat Rev Immunol. 2004 Dec;4(12):931-40. doi: 10.1038/nri1497. Review. PubMed PMID: 15573128.

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Rothrock CR, House AE, Lynch KW. HnRNP L represses exon splicing via a regulated exonic splicing silencer. EMBO J. 2005 Aug 3;24(15):2792-802. doi: 10.1038/sj.emboj.7600745. Epub 2005 Jul 7. PubMed PMID: 16001081; PubMed Central PMCID: PMC1182240.

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Tong A, Nguyen J, Lynch KW. Differential expression of CD45 isoforms is controlled by the combined activity of basal and inducible splicing-regulatory elements in each of the variable exons. J Biol Chem. 2005 Nov 18;280(46):38297-304. doi: 10.1074/jbc.M508123200. Epub 2005 Sep 19. PubMed PMID: 16172127.

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Levinson N, Hinman R, Patil A, Stephenson CR, Werner S, Woo GH, Xiao J, Wipf P, Lynch KW. Use of transcriptional synergy to augment sensitivity of a splicing reporter assay. RNA. 2006 May;12(5):925-30. doi: 10.1261/rna.8306. Epub 2006 Mar 23. PubMed PMID: 16556940; PubMed Central PMCID: PMC1440914.

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House AE, Lynch KW. An exonic splicing silencer represses spliceosome assembly after ATP-dependent exon recognition. Nat Struct Mol Biol. 2006 Oct;13(10):937-44. doi: 10.1038/nsmb1149. Epub 2006 Sep 24. PubMed PMID: 16998487.

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Lynch KW. Cotranscriptional splicing regulation: it's not just about speed. Nat Struct Mol Biol. 2006 Nov;13(11):952-3. doi: 10.1038/nsmb1106-952. PubMed PMID: 17082788.

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Johnson EB, Steffen DJ, Lynch KW, Herz J. Defective splicing of Megf7/Lrp4, a regulator of distal limb development, in autosomal recessive mulefoot disease. Genomics. 2006 Nov;88(5):600-9. doi: 10.1016/j.ygeno.2006.08.005. Epub 2006 Sep 11. PubMed PMID: 16963222.

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Lynch KW. Regulation of alternative splicing by signal transduction pathways. Adv Exp Med Biol. 2007;623:161-74. doi: 10.1007/978-0-387-77374-2_10. Review. PubMed PMID: 18380346.

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Ip JY, Tong A, Pan Q, Topp JD, Blencowe BJ, Lynch KW. Global analysis of alternative splicing during T-cell activation. RNA. 2007 Apr;13(4):563-72. doi: 10.1261/rna.457207. Epub 2007 Feb 16. PubMed PMID: 17307815; PubMed Central PMCID: PMC1831861.

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Melton AA, Jackson J, Wang J, Lynch KW. Combinatorial control of signal-induced exon repression by hnRNP L and PSF. Mol Cell Biol. 2007 Oct;27(19):6972-84. doi: 10.1128/MCB.00419-07. Epub 2007 Jul 30. PubMed PMID: 17664280; PubMed Central PMCID: PMC2099238.

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House AE, Lynch KW. Regulation of alternative splicing: more than just the ABCs. J Biol Chem. 2008 Jan 18;283(3):1217-21. doi: 10.1074/jbc.R700031200. Epub 2007 Nov 16. Review. PubMed PMID: 18024429.

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Topp JD, Jackson J, Melton AA, Lynch KW. A cell-based screen for splicing regulators identifies hnRNP LL as a distinct signal-induced repressor of CD45 variable exon 4. RNA. 2008 Oct;14(10):2038-49. doi: 10.1261/rna.1212008. Epub 2008 Aug 21. PubMed PMID: 18719244; PubMed Central PMCID: PMC2553740.

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Heyd F, Lynch KW. Getting under the skin of alternative splicing: identification of epithelial-specific splicing factors. Mol Cell. 2009 Mar 27;33(6):674-6. doi: 10.1016/j.molcel.2009.03.001. PubMed PMID: 19328061.

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Motta-Mena LB, Heyd F, Lynch KW. Context-dependent regulatory mechanism of the splicing factor hnRNP L. Mol Cell. 2010 Jan 29;37(2):223-34. doi: 10.1016/j.molcel.2009.12.027. PubMed PMID: 20122404; PubMed Central PMCID: PMC2818868.

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Heyd F, Lynch KW. Phosphorylation-dependent regulation of PSF by GSK3 controls CD45 alternative splicing. Mol Cell. 2010 Oct 8;40(1):126-37. doi: 10.1016/j.molcel.2010.09.013. PubMed PMID: 20932480; PubMed Central PMCID: PMC2954053.

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Shankarling G, Lynch KW. Living or dying by RNA processing: caspase expression in NSCLC. J Clin Invest. 2010 Nov;120(11):3798-801. doi: 10.1172/JCI45037. Epub 2010 Oct 25. PubMed PMID: 20972326; PubMed Central PMCID: PMC2965003.

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Mallory MJ, Jackson J, Weber B, Chi A, Heyd F, Lynch KW. Signal- and development-dependent alternative splicing of LEF1 in T cells is controlled by CELF2. Mol Cell Biol. 2011 Jun;31(11):2184-95. doi: 10.1128/MCB.05170-11. Epub 2011 Mar 28. PubMed PMID: 21444716; PubMed Central PMCID: PMC3133246.

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Motta-Mena LB, Smith SA, Mallory MJ, Jackson J, Wang J, Lynch KW. A disease-associated polymorphism alters splicing of the human CD45 phosphatase gene by disrupting combinatorial repression by heterogeneous nuclear ribonucleoproteins (hnRNPs). J Biol Chem. 2011 Jun 3;286(22):20043-53. doi: 10.1074/jbc.M111.218727. Epub 2011 Apr 20. PubMed PMID: 21507955; PubMed Central PMCID: PMC3103377.

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Heyd F, Lynch KW. Degrade, move, regroup: signaling control of splicing proteins. Trends Biochem Sci. 2011 Aug;36(8):397-404. doi: 10.1016/j.tibs.2011.04.003. Epub 2011 May 17. Review. PubMed PMID: 21596569; PubMed Central PMCID: PMC3155649.

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Heyd F, Lynch KW. PSF controls expression of histone variants and cellular viability in thymocytes. Biochem Biophys Res Commun. 2011 Nov 4;414(4):743-9. doi: 10.1016/j.bbrc.2011.09.149. Epub 2011 Oct 6. PubMed PMID: 22001927; PubMed Central PMCID: PMC3210398.

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Martinez NM, Pan Q, Cole BS, Yarosh CA, Babcock GA, Heyd F, Zhu W, Ajith S, Blencowe BJ, Lynch KW. Alternative splicing networks regulated by signaling in human T cells. RNA. 2012 May;18(5):1029-40. doi: 10.1261/rna.032243.112. Epub 2012 Mar 27. PubMed PMID: 22454538; PubMed Central PMCID: PMC3334690.

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Chiou NT, Shankarling G, Lynch KW. hnRNP L and hnRNP A1 induce extended U1 snRNA interactions with an exon to repress spliceosome assembly. Mol Cell. 2013 Mar 7;49(5):972-82. doi: 10.1016/j.molcel.2012.12.025. Epub 2013 Feb 7. PubMed PMID: 23394998; PubMed Central PMCID: PMC3595347.

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Vu NT, Park MA, Shultz JC, Goehe RW, Hoeferlin LA, Shultz MD, Smith SA, Lynch KW, Chalfant CE. hnRNP U enhances caspase-9 splicing and is modulated by AKT-dependent phosphorylation of hnRNP L. J Biol Chem. 2013 Mar 22;288(12):8575-8584. doi: 10.1074/jbc.M112.443333. Epub 2013 Feb 8. PubMed PMID: 23396972; PubMed Central PMCID: PMC3605676.

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Martinez NM, Lynch KW. Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn. Immunol Rev. 2013 May;253(1):216-36. doi: 10.1111/imr.12047. Review. PubMed PMID: 23550649; PubMed Central PMCID: PMC3621013.

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Tsai PL, Chiou NT, Kuss S, García-Sastre A, Lynch KW, Fontoura BM. Cellular RNA binding proteins NS1-BP and hnRNP K regulate influenza A virus RNA splicing. PLoS Pathog. 2013;9(6):e1003460. doi: 10.1371/journal.ppat.1003460. Epub 2013 Jun 27. PubMed PMID: 23825951; PubMed Central PMCID: PMC3694860.

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Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311. PubMed PMID: 23846655; PubMed Central PMCID: PMC3929597.

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Shankarling G, Lynch KW. Minimal functional domains of paralogues hnRNP L and hnRNP LL exhibit mechanistic differences in exonic splicing repression. Biochem J. 2013 Jul 15;453(2):271-9. doi: 10.1042/BJ20130432. PubMed PMID: 23646903; PubMed Central PMCID: PMC4069513.

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Smith SA, Ray D, Cook KB, Mallory MJ, Hughes TR, Lynch KW. Paralogs hnRNP L and hnRNP LL exhibit overlapping but distinct RNA binding constraints. PLoS One. 2013;8(11):e80701. doi: 10.1371/journal.pone.0080701. eCollection 2013. PubMed PMID: 24244709; PubMed Central PMCID: PMC3823766.

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Chiou NT, Lynch KW. Mechanisms of spliceosomal assembly. Methods Mol Biol. 2014;1126:35-43. doi: 10.1007/978-1-62703-980-2_3. PubMed PMID: 24549654.

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Smith SA, Lynch KW. Cell-based splicing of minigenes. Methods Mol Biol. 2014;1126:243-55. doi: 10.1007/978-1-62703-980-2_18. PubMed PMID: 24549669.

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Shankarling G, Cole BS, Mallory MJ, Lynch KW. Transcriptome-wide RNA interaction profiling reveals physical and functional targets of hnRNP L in human T cells. Mol Cell Biol. 2014 Jan;34(1):71-83. doi: 10.1128/MCB.00740-13. Epub 2013 Oct 28. PubMed PMID: 24164894; PubMed Central PMCID: PMC3911283.

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Motta-Mena LB, Reade A, Mallory MJ, Glantz S, Weiner OD, Lynch KW, Gardner KH. An optogenetic gene expression system with rapid activation and deactivation kinetics. Nat Chem Biol. 2014 Mar;10(3):196-202. doi: 10.1038/nchembio.1430. Epub 2014 Jan 12. PubMed PMID: 24413462; PubMed Central PMCID: PMC3944926.

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Gazzara MR, Vaquero-Garcia J, Lynch KW, Barash Y. In silico to in vivo splicing analysis using splicing code models. Methods. 2014 May 1;67(1):3-12. doi: 10.1016/j.ymeth.2013.11.006. Epub 2013 Dec 7. PubMed PMID: 24321485; PubMed Central PMCID: PMC4321995.

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Moy RH, Cole BS, Yasunaga A, Gold B, Shankarling G, Varble A, Molleston JM, tenOever BR, Lynch KW, Cherry S. Stem-loop recognition by DDX17 facilitates miRNA processing and antiviral defense. Cell. 2014 Aug 14;158(4):764-777. doi: 10.1016/j.cell.2014.06.023. PubMed PMID: 25126784; PubMed Central PMCID: PMC4134512.

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Lynch KW. Thoughts on NGS, alternative splicing and what we still need to know. RNA. 2015 Apr;21(4):683-4. doi: 10.1261/rna.050419.115. PubMed PMID: 25780190; PubMed Central PMCID: PMC4371332.

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Mallory MJ, Allon SJ, Qiu J, Gazzara MR, Tapescu I, Martinez NM, Fu XD, Lynch KW. Induced transcription and stability of CELF2 mRNA drives widespread alternative splicing during T-cell signaling. Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):E2139-48. doi: 10.1073/pnas.1423695112. Epub 2015 Apr 13. PubMed PMID: 25870297; PubMed Central PMCID: PMC4418860.

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Yarosh CA, Iacona JR, Lutz CS, Lynch KW. PSF: nuclear busy-body or nuclear facilitator?. Wiley Interdiscip Rev RNA. 2015 Jul-Aug;6(4):351-67. doi: 10.1002/wrna.1280. Epub 2015 Apr 1. Review. PubMed PMID: 25832716; PubMed Central PMCID: PMC4478221.

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Martinez NM, Agosto L, Qiu J, Mallory MJ, Gazzara MR, Barash Y, Fu XD, Lynch KW. Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation. Genes Dev. 2015 Oct 1;29(19):2054-66. doi: 10.1101/gad.267245.115. PubMed PMID: 26443849; PubMed Central PMCID: PMC4604346.

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Yarosh CA, Tapescu I, Thompson MG, Qiu J, Mallory MJ, Fu XD, Lynch KW. TRAP150 interacts with the RNA-binding domain of PSF and antagonizes splicing of numerous PSF-target genes in T cells. Nucleic Acids Res. 2015 Oct 15;43(18):9006-16. doi: 10.1093/nar/gkv816. Epub 2015 Aug 10. PubMed PMID: 26261210; PubMed Central PMCID: PMC4605305.