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Publications

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  1. Xu H, Fair BJ, Dwyer ZW, Gildea M, Pleiss JA.  2019.  Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing.  Nature Methods.  2019 Jan;16(1):55-58.  PMID: 30573814.  PDF
  2. Thakran P, Pandit PA, Datta S, Kolathur KK, Pleiss JA, Mishra SK. 2018. Sde2 is an intron-specific pre-mRNA splicing regulator activated by ubiquitin-like processing.  EMBO J.  2018 Jan 4;37(1):89-101.  PMID: 28947618.  PDF
  3. Yeh CS, Chang SL, Chen JH, Wang HK, Chou YC, Wang CH, Huang SH, Larson A, Pleiss JA, Chang WH, Chang TH.  2017.  The conserved AU dinucleotide at the 5′ end of nascent U1 snRNA is optimized for the interaction with nuclear cap-binding-complex.  Nucleic Acids Res. 2017 Sep 19;45(16):9679-9693.  PMID: 28934473.  PDF
  4. Mayerle M, Raghavan M, Ledoux S, Price A, Stepankiw N, Hadjivassilioua H, Moehle EA, Mendoza SD, Pleiss JA*, Guthrie C*, Abelson J*. 2017. Structural toggle in the RNaseH domain of Prp8 helps balance splicing fidelity and catalytic efficiency.  PNAS.  doi: 10.1073/pnas.1701462114.  PMID: 28416677.  PDF
  5. Fair BJ and Pleiss JA*. 2016. The power of fission: yeast as a tool for understanding complex splicing.  Current Genetics. doi:10.1007/s00294-016-0647-6.  PMID: 27628706.  PDF
  6. Inada M*, Nichols RJ, Parsa J-Y, Homer CM, Benn RA, Hoxie RS, Madhani H, Shuman S, Schwer B, and Pleiss JA*. 2016. Phospho-site mutants of the RNA Polymerase II C-terminal domain alter subtelomeric gene expression and chromatin modification state in fission yeast.  Nucleic Acids Research, 2016 Jul 8. pii: gkw603.  PMID: 27402158.  PDF
  7. Larson A, Fair BJ, and Pleiss JA*. 2016. A sequencing based reverse genetic screen for pre-mRNA splicing mutants reveals interconnections between RNA-processing pathways in fission yeast.  G3, 6(6):1513-23.  PMID: 27172183. PDF
  8. Alfonso C, Ahmed Y, Degner E, Pleiss JA, Wolfner MF, and Harrington LC. 2016. Mating-Induced Transcriptome Changes in the Reproductive Tract of Female Aedes aegypti. PLoS Neglected Tropical Diseases, 10(2):e0004451.  doi: 10.1371/journal.pntd.0004451.  PMCID: PMC4764262.  PDF
  9. Vo TV, Das J, Meyer MJ, Cordero NA, Akturk N, Fair BJ, Degatano AG, Fragoza R, Choate LA, Liu LG, Matsuyama A, Trickey M, Grimson A, Yamano H, Yoshida M, Wei X, Roth FP, Pleiss JA, Xia Y, and Yu H. 2016. A proteome-wide fission yeast interactome map reveals network evolution principles from yeasts to human.  Cell, 164(1-2):310-23.  PMCID: PMC4715267. PDF
  10. Stepankiw N, Raghavan M, Grimson A*, and Pleiss JA*. 2015. Widespread Alternative and Aberrant Splicing Revealed by Lariat Sequencing.  Nucleic Acids Research, 43(17):8488-501.  PMID: 26261211. PDF
  11. Henne WM, Balogi Z, Zhu L, Stefan C, Pleiss JA, and Emr SD. 2015. Mdm1/Snx13 is a novel ER-endolysosomal inter-organelle tethering protein.  Journal of Cell Biology, 210(4):541-51.  PMCID: PMC4539980. PDF
  12. Cui J, Sartain C, Pleiss JA*, Wolfner MF*. 2013. Cytoplasmic polyadenylation is a major mRNA regulator during oogenesis and egg activation in Drosophila.  Dev. Biology, doi:pii: S0012-1606(13)00438-7. 10.1016/j.ydbio.2013.08.013.  PMCID: PMC3821703. PDF
  13. Das J, Vo TV, Wei X, Mellor JC, Tong V, Degatano AG, Wang X, Wang L, Cordero NA, Kruer-Zerhusen N, Matsuyama A, Pleiss JA, Lipkin SM, Yoshida M, Roth FP, Yu H. 2013. Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways. Sci Signal. 6(276):ra38. doi: 10.1126/scisignal.2003350.  PMCID: PMC3777727. PDF
  14. Awan AR, Manfredo A, Pleiss JA*. 2013. Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans.  PNAS, 110(31):12762-7.  PMCID: PMC3732940. PDF
  15. Weiner A, Chen H, Liu CL, Rahat A, Klein A, Soares L, Gudipati M, Pfeffner J, Regev A, Buratowski S, Pleiss JA, Friedman N, Rando OJ. 2012. Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biology, 10(7):e1001369. doi: 10.1371/journal.pbio.1001369.  PMCID: PMC3416867. PDF
  16. Albulescu L-O, Sabet N, Gudipati M, Stepankiw N, Bergman ZJ, Huffaker TC, Pleiss JA*. 2012. A Quantitative, High-Throughput Reverse Genetic Screen Reveals Novel Connections Between pre-mRNA Splicing and 5′ and 3′-End Transcript Determinants.  PLoS Genetics, 8(3):e1002530.  PMCID: PMC3315463. PDF
  17. Inada M and Pleiss JA*. 2010. Genome-Wide Approaches to Monitor Pre-mRNA Splicing. Methods in Enzymology.  Guide to Yeast Genetics: Functional Genomics, Proteomics, and Other Systems Analysis Volume 470, 51-75.  PMID 20946806.  PDF
  18. Abelson J, Blanco M, Ditzler MA, Fuller F, Aravamudhan P, Wood M, Villa T, Ryan DE, Pleiss JA, Maeder C, Guthrie C, Walter NG. 2010. Conformational Dynamics of Single pre-mRNA Molecules in Spliceosome Assembly. Nature Structural and Molecular Biology  17(4):504-12.  PMID: 20305654. PDF
  19. Sahi C, Lee T, Inada M, Pleiss JA, Craig EA. 2010. Cwc23, an essential J protein critical for pre-mRNA splicing with a dispensable J domain. Mol. Cell. Biol 30, 33-42.  PMID: 19822657. PDF
  20. Zhang L, Xu T, Maeder C, Bud L-O, Shanks J, Nix J, Guthrie C, Pleiss JA, Zhao R. 2009. Structural evidence for consecutive Hel308-like modules in the spliceosomal ATPase Brr2.  Nature Structural and Molecular Biology, 16(7):731-9.  PMID: 19525970. PDF
  21. Coughlin DJ, Pleiss JA, Whitworth GB, Engelke DR. 2008. Genome-wide search for yeast RNase P substrates reveals role in maturation of intron-encoded box C/D small nucleolar RNAs.  PNAS  105(34):12218-23.  PMID: 18713869. PDF
  22. Pleiss JA, Whitworth G, Bergkessel M, and Guthrie C. 2007. Rapid, transcript-specific changes in splicing in response to environmental stress.  Molecular Cell  27(6):928-37.  PMID: 17889666. PDF
  23. Pleiss JA, Whitworth G, Bergkessel M, and Guthrie C. 2007. Transcript-specificity in Yeast pre-mRNA Splicing Revealed by Mutations in Core Spliceosomal Components.  PLoS Biology 5, e90 doi:10.1371/journal.pbio.0050090.  PMID: 17388687. PDF
  24. Stark MR+, Pleiss JA+, Deras M, Scaringe SA, and Rader SD. 2006. An RNA-ligase mediated method for the efficient creation of large, synthetic RNAs.  RNA  12, 2014-2019. PDF
  25. Villa T, Pleiss JA, and Guthrie C. 2002. Spliceosomal snRNAs:  Mg2+-dependent chemistry at the catalytic core?  Cell  109, 149-152. PDF
  26. Wolfson AD, LaRiviere FJ, Pleiss JA, Dale T, Asahara H, and Uhlenbeck OC. 2002. tRNA Conformity.  Cold Spring Harbor Symposia on Quantitative Biology:  The Ribosome  (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY)  66, 185-193.  PDF
  27. Pleiss JA and Uhlenbeck OC. 2001. Identification of thermodynamically relevant interactions between EF-Tu and backbone elements of tRNA.  Journal of Molecular Biology  308, 895-905. PDF
  28. Pleiss JA, Wolfson AD, and Uhlenbeck OC. 2000. Mapping contacts between E. coli alanyl tRNA synthetase and 2’ hydroxyls using a complete tRNA molecule.  Biochemistry  39, 8250-8258. PDF
  29. Piepenburg O, Pape T, Pleiss JA, Wintermeyer W, Uhlenbeck OC, and Rodnina MV. 2000. Intact aa-tRNA is required to trigger the GTPase of EF-Tu on the ribosome.  Biochemistry  39, 1734-1738. PDF
  30. Pleiss JA, Derrick MS, Uhlenbeck OC. 1998. T7 RNA polymerase produces 5′ end heterogeneity during in vitro transcription from certain templates.  RNA  4, 1313-1317. PDF
  31. Wolfson AD, Pleiss JA, Uhlenbeck OC. 1998. A new assay for tRNA aminoacylation kinetics.  RNA  4, 1019-1023. PDF