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Items: 1 to 50 of 64

1.

Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing.

Agosto LM, Gazzara MR, Radens CM, Sidoli S, Baeza J, Garcia BA, Lynch KW.

Genome Res. 2019 Nov 14. doi: 10.1101/gr.248435.119. [Epub ahead of print]

PMID:
31727681
2.

RNA Binding Protein CELF2 Regulates Signal-Induced Alternative Polyadenylation by Competing with Enhancers of the Polyadenylation Machinery.

Chatrikhi R, Mallory MJ, Gazzara MR, Agosto LM, Zhu WS, Litterman AJ, Ansel KM, Lynch KW.

Cell Rep. 2019 Sep 10;28(11):2795-2806.e3. doi: 10.1016/j.celrep.2019.08.022.

3.

Structural-functional interactions of NS1-BP protein with the splicing and mRNA export machineries for viral and host gene expression.

Zhang K, Shang G, Padavannil A, Wang J, Sakthivel R, Chen X, Kim M, Thompson MG, García-Sastre A, Lynch KW, Chen ZJ, Chook YM, Fontoura BMA.

Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):E12218-E12227. doi: 10.1073/pnas.1818012115. Epub 2018 Dec 11.

4.

Aberrant splicing in B-cell acute lymphoblastic leukemia.

Black KL, Naqvi AS, Asnani M, Hayer KE, Yang SY, Gillespie E, Bagashev A, Pillai V, Tasian SK, Gazzara MR, Carroll M, Taylor D, Lynch KW, Barash Y, Thomas-Tikhonenko A.

Nucleic Acids Res. 2019 Jan 25;47(2):1043. doi: 10.1093/nar/gky1231. No abstract available.

5.

Aberrant splicing in B-cell acute lymphoblastic leukemia.

Black KL, Naqvi AS, Asnani M, Hayer KE, Yang SY, Gillespie E, Bagashev A, Pillai V, Tasian SK, Gazzara MR, Carroll M, Taylor D, Lynch KW, Barash Y, Thomas-Tikhonenko A.

Nucleic Acids Res. 2018 Nov 30;46(21):11357-11369. doi: 10.1093/nar/gky946. Erratum in: Nucleic Acids Res. 2019 Jan 25;47(2):1043.

6.

Alternative pre-mRNA splicing switch controls hESC pluripotency and differentiation.

Agosto LM, Lynch KW.

Genes Dev. 2018 Sep 1;32(17-18):1103-1104. doi: 10.1101/gad.318451.118. Review.

7.

Co-regulatory activity of hnRNP K and NS1-BP in influenza and human mRNA splicing.

Thompson MG, Muñoz-Moreno R, Bhat P, Roytenberg R, Lindberg J, Gazzara MR, Mallory MJ, Zhang K, García-Sastre A, Fontoura BMA, Lynch KW.

Nat Commun. 2018 Jun 19;9(1):2407. doi: 10.1038/s41467-018-04779-4.

8.

HnRNP L represses cryptic exons.

McClory SP, Lynch KW, Ling JP.

RNA. 2018 Jun;24(6):761-768. doi: 10.1261/rna.065508.117. Epub 2018 Mar 26.

9.

Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing.

Shinde MY, Sidoli S, Kulej K, Mallory MJ, Radens CM, Reicherter AL, Myers RL, Barash Y, Lynch KW, Garcia BA, Klein PS.

J Biol Chem. 2017 Nov 3;292(44):18240-18255. doi: 10.1074/jbc.M117.813527. Epub 2017 Sep 15.

10.

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes.

Gazzara MR, Mallory MJ, Roytenberg R, Lindberg JP, Jha A, Lynch KW, Barash Y.

Genome Res. 2017 Aug;27(8):1360-1370. doi: 10.1101/gr.220517.117. Epub 2017 May 16.

11.

Corrigendum: Influenza virus mRNA trafficking through host nuclear speckles.

Mor A, White A, Zhang K, Thompson M, Esparza M, Muñoz-Moreno R, Koide K, Lynch KW, García-Sastre A, Fontoura BM.

Nat Microbiol. 2017 Jan 9;2:17002. doi: 10.1038/nmicrobiol.2017.2. No abstract available.

PMID:
28067239
12.

Influenza virus mRNA trafficking through host nuclear speckles.

Mor A, White A, Zhang K, Thompson M, Esparza M, Muñoz-Moreno R, Koide K, Lynch KW, García-Sastre A, Fontoura BM.

Nat Microbiol. 2016 May 27;1(7):16069. doi: 10.1038/nmicrobiol.2016.69. Erratum in: Nat Microbiol. 2017 Jan 09;2:17002.

13.

Position-dependent activity of CELF2 in the regulation of splicing and implications for signal-responsive regulation in T cells.

Ajith S, Gazzara MR, Cole BS, Shankarling G, Martinez NM, Mallory MJ, Lynch KW.

RNA Biol. 2016 Jun 2;13(6):569-81. doi: 10.1080/15476286.2016.1176663. Epub 2016 Apr 20.

14.

A new view of transcriptome complexity and regulation through the lens of local splicing variations.

Vaquero-Garcia J, Barrera A, Gazzara MR, González-Vallinas J, Lahens NF, Hogenesch JB, Lynch KW, Barash Y.

Elife. 2016 Feb 1;5:e11752. doi: 10.7554/eLife.11752.

15.

Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy.

Sotillo E, Barrett DM, Black KL, Bagashev A, Oldridge D, Wu G, Sussman R, Lanauze C, Ruella M, Gazzara MR, Martinez NM, Harrington CT, Chung EY, Perazzelli J, Hofmann TJ, Maude SL, Raman P, Barrera A, Gill S, Lacey SF, Melenhorst JJ, Allman D, Jacoby E, Fry T, Mackall C, Barash Y, Lynch KW, Maris JM, Grupp SA, Thomas-Tikhonenko A.

Cancer Discov. 2015 Dec;5(12):1282-95. doi: 10.1158/2159-8290.CD-15-1020. Epub 2015 Oct 29.

16.

Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation.

Martinez NM, Agosto L, Qiu J, Mallory MJ, Gazzara MR, Barash Y, Fu XD, Lynch KW.

Genes Dev. 2015 Oct 1;29(19):2054-66. doi: 10.1101/gad.267245.115.

17.

Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons.

Cole BS, Tapescu I, Allon SJ, Mallory MJ, Qiu J, Lake RJ, Fan HY, Fu XD, Lynch KW.

RNA. 2015 Dec;21(12):2053-66. doi: 10.1261/rna.052969.115. Epub 2015 Oct 5.

18.

TRAP150 interacts with the RNA-binding domain of PSF and antagonizes splicing of numerous PSF-target genes in T cells.

Yarosh CA, Tapescu I, Thompson MG, Qiu J, Mallory MJ, Fu XD, Lynch KW.

Nucleic Acids Res. 2015 Oct 15;43(18):9006-16. doi: 10.1093/nar/gkv816. Epub 2015 Aug 10.

19.

Induced transcription and stability of CELF2 mRNA drives widespread alternative splicing during T-cell signaling.

Mallory MJ, Allon SJ, Qiu J, Gazzara MR, Tapescu I, Martinez NM, Fu XD, Lynch KW.

Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):E2139-48. doi: 10.1073/pnas.1423695112. Epub 2015 Apr 13.

20.

PSF: nuclear busy-body or nuclear facilitator?

Yarosh CA, Iacona JR, Lutz CS, Lynch KW.

Wiley Interdiscip Rev RNA. 2015 Jul-Aug;6(4):351-67. doi: 10.1002/wrna.1280. Epub 2015 Apr 1. Review.

21.

Thoughts on NGS, alternative splicing and what we still need to know.

Lynch KW.

RNA. 2015 Apr;21(4):683-4. doi: 10.1261/rna.050419.115. No abstract available.

22.

Stem-loop recognition by DDX17 facilitates miRNA processing and antiviral defense.

Moy RH, Cole BS, Yasunaga A, Gold B, Shankarling G, Varble A, Molleston JM, tenOever BR, Lynch KW, Cherry S.

Cell. 2014 Aug 14;158(4):764-777. doi: 10.1016/j.cell.2014.06.023.

23.

Cell-based splicing of minigenes.

Smith SA, Lynch KW.

Methods Mol Biol. 2014;1126:243-55. doi: 10.1007/978-1-62703-980-2_18.

PMID:
24549669
24.

Mechanisms of spliceosomal assembly.

Chiou NT, Lynch KW.

Methods Mol Biol. 2014;1126:35-43. doi: 10.1007/978-1-62703-980-2_3.

PMID:
24549654
25.

An optogenetic gene expression system with rapid activation and deactivation kinetics.

Motta-Mena LB, Reade A, Mallory MJ, Glantz S, Weiner OD, Lynch KW, Gardner KH.

Nat Chem Biol. 2014 Mar;10(3):196-202. doi: 10.1038/nchembio.1430. Epub 2014 Jan 12.

26.

In silico to in vivo splicing analysis using splicing code models.

Gazzara MR, Vaquero-Garcia J, Lynch KW, Barash Y.

Methods. 2014 May 1;67(1):3-12. doi: 10.1016/j.ymeth.2013.11.006. Epub 2013 Dec 7.

27.

Paralogs hnRNP L and hnRNP LL exhibit overlapping but distinct RNA binding constraints.

Smith SA, Ray D, Cook KB, Mallory MJ, Hughes TR, Lynch KW.

PLoS One. 2013 Nov 11;8(11):e80701. doi: 10.1371/journal.pone.0080701. eCollection 2013.

28.

Transcriptome-wide RNA interaction profiling reveals physical and functional targets of hnRNP L in human T cells.

Shankarling G, Cole BS, Mallory MJ, Lynch KW.

Mol Cell Biol. 2014 Jan;34(1):71-83. doi: 10.1128/MCB.00740-13. Epub 2013 Oct 28.

29.

A compendium of RNA-binding motifs for decoding gene regulation.

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.

Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311.

30.

Cellular RNA binding proteins NS1-BP and hnRNP K regulate influenza A virus RNA splicing.

Tsai PL, Chiou NT, Kuss S, García-Sastre A, Lynch KW, Fontoura BM.

PLoS Pathog. 2013;9(6):e1003460. doi: 10.1371/journal.ppat.1003460. Epub 2013 Jun 27.

31.
32.

Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn.

Martinez NM, Lynch KW.

Immunol Rev. 2013 May;253(1):216-36. doi: 10.1111/imr.12047. Review.

33.

hnRNP U enhances caspase-9 splicing and is modulated by AKT-dependent phosphorylation of hnRNP L.

Vu NT, Park MA, Shultz JC, Goehe RW, Hoeferlin LA, Shultz MD, Smith SA, Lynch KW, Chalfant CE.

J Biol Chem. 2013 Mar 22;288(12):8575-84. doi: 10.1074/jbc.M112.443333. Epub 2013 Feb 8.

34.

hnRNP L and hnRNP A1 induce extended U1 snRNA interactions with an exon to repress spliceosome assembly.

Chiou NT, Shankarling G, Lynch KW.

Mol Cell. 2013 Mar 7;49(5):972-82. doi: 10.1016/j.molcel.2012.12.025. Epub 2013 Feb 7.

35.

Alternative splicing networks regulated by signaling in human T cells.

Martinez NM, Pan Q, Cole BS, Yarosh CA, Babcock GA, Heyd F, Zhu W, Ajith S, Blencowe BJ, Lynch KW.

RNA. 2012 May;18(5):1029-40. doi: 10.1261/rna.032243.112. Epub 2012 Mar 27.

36.

PSF controls expression of histone variants and cellular viability in thymocytes.

Heyd F, Lynch KW.

Biochem Biophys Res Commun. 2011 Nov 4;414(4):743-9. doi: 10.1016/j.bbrc.2011.09.149. Epub 2011 Oct 6.

37.

Degrade, move, regroup: signaling control of splicing proteins.

Heyd F, Lynch KW.

Trends Biochem Sci. 2011 Aug;36(8):397-404. doi: 10.1016/j.tibs.2011.04.003. Epub 2011 May 17. Review.

38.

A disease-associated polymorphism alters splicing of the human CD45 phosphatase gene by disrupting combinatorial repression by heterogeneous nuclear ribonucleoproteins (hnRNPs).

Motta-Mena LB, Smith SA, Mallory MJ, Jackson J, Wang J, Lynch KW.

J Biol Chem. 2011 Jun 3;286(22):20043-53. doi: 10.1074/jbc.M111.218727. Epub 2011 Apr 20.

39.

Signal- and development-dependent alternative splicing of LEF1 in T cells is controlled by CELF2.

Mallory MJ, Jackson J, Weber B, Chi A, Heyd F, Lynch KW.

Mol Cell Biol. 2011 Jun;31(11):2184-95. doi: 10.1128/MCB.05170-11. Epub 2011 Mar 28.

40.

Living or dying by RNA processing: caspase expression in NSCLC.

Shankarling G, Lynch KW.

J Clin Invest. 2010 Nov;120(11):3798-801. doi: 10.1172/JCI45037. Epub 2010 Oct 25.

41.

Phosphorylation-dependent regulation of PSF by GSK3 controls CD45 alternative splicing.

Heyd F, Lynch KW.

Mol Cell. 2010 Oct 8;40(1):126-37. doi: 10.1016/j.molcel.2010.09.013.

42.

Context-dependent regulatory mechanism of the splicing factor hnRNP L.

Motta-Mena LB, Heyd F, Lynch KW.

Mol Cell. 2010 Jan 29;37(2):223-34. doi: 10.1016/j.molcel.2009.12.027.

43.

Getting under the skin of alternative splicing: identification of epithelial-specific splicing factors.

Heyd F, Lynch KW.

Mol Cell. 2009 Mar 27;33(6):674-6. doi: 10.1016/j.molcel.2009.03.001.

44.

A cell-based screen for splicing regulators identifies hnRNP LL as a distinct signal-induced repressor of CD45 variable exon 4.

Topp JD, Jackson J, Melton AA, Lynch KW.

RNA. 2008 Oct;14(10):2038-49. doi: 10.1261/rna.1212008. Epub 2008 Aug 21.

45.

Regulation of alternative splicing by signal transduction pathways.

Lynch KW.

Adv Exp Med Biol. 2007;623:161-74. Review.

PMID:
18380346
46.

Regulation of alternative splicing: more than just the ABCs.

House AE, Lynch KW.

J Biol Chem. 2008 Jan 18;283(3):1217-21. Epub 2007 Nov 16. Review.

47.

Science at the interface of chemistry and biology at the University of Texas Southwestern Medical Center.

Ready JM, Lynch KW.

ACS Chem Biol. 2007 Aug 17;2(8):512-4. No abstract available.

PMID:
17708664
48.

Combinatorial control of signal-induced exon repression by hnRNP L and PSF.

Melton AA, Jackson J, Wang J, Lynch KW.

Mol Cell Biol. 2007 Oct;27(19):6972-84. Epub 2007 Jul 30.

49.

Global analysis of alternative splicing during T-cell activation.

Ip JY, Tong A, Pan Q, Topp JD, Blencowe BJ, Lynch KW.

RNA. 2007 Apr;13(4):563-72. Epub 2007 Feb 16.

50.

Cotranscriptional splicing regulation: it's not just about speed.

Lynch KW.

Nat Struct Mol Biol. 2006 Nov;13(11):952-3. No abstract available.

PMID:
17082788

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