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Craig D. Kaplan - Publications

Affiliations: 
2003 Harvard University, Cambridge, MA, United States 
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52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G. Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 Å using a free-electron laser. Biorxiv : the Preprint Server For Biology. PMID 37790421 DOI: 10.1101/2023.09.22.559052  0.392
2023 Kaplan CD. Mediator and Pol II go to eleven (CTD repeats). Proceedings of the National Academy of Sciences of the United States of America. 120: e2304596120. PMID 37094154 DOI: 10.1073/pnas.2304596120  0.328
2023 Dutagaci B, Duan B, Qiu C, Kaplan CD, Feig M. Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning. Plos Computational Biology. 19: e1010999. PMID 36947548 DOI: 10.1371/journal.pcbi.1010999  0.305
2023 Chung C, Verheijen BM, Navapanich Z, McGann EG, Shemtov S, Lai GJ, Arora P, Towheed A, Haroon S, Holczbauer A, Chang S, Manojlovic Z, Simpson S, Thomas KW, Kaplan C, et al. Evolutionary conservation of the fidelity of transcription. Nature Communications. 14: 1547. PMID 36941254 DOI: 10.1038/s41467-023-36525-w  0.351
2023 Duan B, Qiu C, Sze SH, Kaplan C. Widespread epistasis shapes RNA Polymerase II active site function and evolution. Biorxiv : the Preprint Server For Biology. PMID 36909581 DOI: 10.1101/2023.02.27.530048  0.464
2022 Bassett J, Rimel JK, Basu S, Basnet P, Luo J, Engel KL, Nagel M, Woyciehowsky A, Ebmeier CC, Kaplan CD, Taatjes DJ, Ranish JA. Systematic mutagenesis of TFIIH subunit p52/Tfb2 identifies residues required for XPB/Ssl2 subunit function and genetic interactions with TFB6. The Journal of Biological Chemistry. 102433. PMID 36041630 DOI: 10.1016/j.jbc.2022.102433  0.472
2022 Yang C, Fujiwara R, Kim HJ, Basnet P, Zhu Y, Gorbea Colón JJ, Steimle S, Garcia BA, Kaplan CD, Murakami K. Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Molecular Cell. PMID 35051353 DOI: 10.1016/j.molcel.2021.12.020  0.512
2021 Zhao T, Vvedenskaya IO, Lai WK, Basu S, Pugh BF, Nickels BE, Kaplan CD. Ssl2/TFIIH function in transcription start site scanning by RNA Polymerase II in . Elife. 10. PMID 34652274 DOI: 10.7554/eLife.71013  0.478
2021 Kaplan CD, Arndt KM. A PICture is worth a thousand words (and ten references). Cell. 184: 3850-3851. PMID 34297929 DOI: 10.1016/j.cell.2021.06.030  0.611
2020 Qiu C, Jin H, Vvedenskaya I, Llenas JA, Zhao T, Malik I, Visbisky AM, Schwartz SL, Cui P, Čabart P, Han KH, Lai WKM, Metz RP, Johnson CD, Sze SH, ... ... Kaplan CD, et al. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome Biology. 21: 132. PMID 32487207 DOI: 10.1186/S13059-020-02040-0  0.498
2020 Leng X, Ivanov M, Kindgren P, Malik I, Thieffry A, Brodersen P, Sandelin A, Kaplan CD, Marquardt S. Organismal benefits of transcription speed control at gene boundaries. Embo Reports. e49315. PMID 32103605 DOI: 10.15252/Embr.201949315  0.525
2019 Chen Z, Gabizon R, Brown AI, Lee A, Song A, Diaz-Celis C, Kaplan CD, Koslover EF, Yao T, Bustamante C. High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier. Elife. 8. PMID 31364986 DOI: 10.7554/Elife.48281  0.417
2019 Qiu C, Kaplan CD. Functional assays for transcription mechanisms in high-throughput. Methods (San Diego, Calif.). PMID 30797033 DOI: 10.1016/j.ymeth.2019.02.017  0.353
2018 Maitra N, Anandhakumar J, Blank HM, Kaplan CD, Polymenis M. Perturbations of Transcription and Gene Expression-Associated Processes Alter Distribution of Cell Size Values in . G3 (Bethesda, Md.). PMID 30463882 DOI: 10.1534/G3.118.200854  0.39
2018 Qiu C, Erinne OC, Dave JM, Cui P, Jin H, Muthukrishnan N, Tang LK, Ganesh Babu S, Lam KC, Vandeventer PJ, Strohner R, Van den Brulle J, Sze SH, Kaplan CD. Correction: High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop. Plos Genetics. 14: e1007158. PMID 29298339 DOI: 10.1371/Journal.Pgen.1007158  0.447
2017 Malik I, Qiu C, Snavely T, Kaplan CD. Wide-ranging and unexpected consequences of altered Pol II catalytic activity in vivo. Nucleic Acids Research. PMID 28119420 DOI: 10.1093/Nar/Gkx037  0.532
2016 Qiu C, Erinne OC, Dave JM, Cui P, Jin H, Muthukrishnan N, Tang LK, Babu SG, Lam KC, Vandeventer PJ, Strohner R, Van den Brulle J, Sze SH, Kaplan CD. High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop. Plos Genetics. 12: e1006321. PMID 27898685 DOI: 10.1371/Journal.Pgen.1006321  0.514
2016 Kaplan CD. Pairs of promoter pairs in a web of transcription. Nature Genetics. 48: 975-6. PMID 27573684 DOI: 10.1038/Ng.3649  0.484
2016 Bird JG, Zhang Y, Tian Y, Panova N, Barvík I, Greene L, Liu M, Buckley B, Krásný L, Lee JK, Kaplan CD, Ebright RH, Nickels BE. The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA. Nature. PMID 27383794 DOI: 10.1038/Nature18622  0.551
2016 Cui P, Jin H, Vutukuru MR, Kaplan CD. Relationships Between RNA Polymerase II Activity and Spt Elongation Factors to Spt- Phenotype and Growth in Saccharomyces cerevisiae. G3 (Bethesda, Md.). PMID 27261007 DOI: 10.1534/G3.116.030346  0.62
2016 Kaster BC, Knippa KC, Kaplan CD, Peterson DO. RNA Polymerase II Trigger Loop Mobility: Indirect Effects of Rpb9. The Journal of Biological Chemistry. PMID 27226557 DOI: 10.1074/Jbc.M116.714394  0.504
2015 Barnes CO, Calero M, Malik I, Graham BW, Spahr H, Lin G, Cohen AE, Brown IS, Zhang Q, Pullara F, Trakselis MA, Kaplan CD, Calero G. Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble. Molecular Cell. 59: 258-69. PMID 26186291 DOI: 10.1016/J.Molcel.2015.06.034  0.569
2015 Murakami K, Mattei PJ, Davis RE, Jin H, Kaplan CD, Kornberg RD. Uncoupling Promoter Opening from Start-Site Scanning. Molecular Cell. 59: 133-8. PMID 26073544 DOI: 10.1016/J.Molcel.2015.05.021  0.578
2015 Jeronimo C, Watanabe S, Kaplan CD, Peterson CL, Robert F. The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations. Molecular Cell. 58: 1113-23. PMID 25959393 DOI: 10.1016/J.Molcel.2015.03.030  0.482
2014 Čabart P, Jin H, Li L, Kaplan CD. Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis. Transcription. 5: e28869. PMID 25764335 DOI: 10.4161/trns.28869  0.477
2014 Jin H, Kaplan CD. Relationships of RNA polymerase II genetic interactors to transcription start site usage defects and growth in Saccharomyces cerevisiae. G3 (Bethesda, Md.). 5: 21-33. PMID 25380729 DOI: 10.1534/G3.114.015180  0.502
2014 Schweikhard V, Meng C, Murakami K, Kaplan CD, Kornberg RD, Block SM. Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms. Proceedings of the National Academy of Sciences of the United States of America. 111: 6642-7. PMID 24733897 DOI: 10.1073/Pnas.1405181111  0.572
2014 Pai DA, Kaplan CD, Kweon HK, Murakami K, Andrews PC, Engelke DR. RNAs nonspecifically inhibit RNA polymerase II by preventing binding to the DNA template. Rna (New York, N.Y.). 20: 644-55. PMID 24614752 DOI: 10.1261/Rna.040444.113  0.529
2014 Schweikhard V, Meng CA, Murakami K, Kaplan CD, Kornberg RD, Block SM. TFIIF and TFIIS Enhance the Mechanical Persistence of Transcript Elongation by RNA Polymerase II Biophysical Journal. 106: 486a. DOI: 10.1016/J.Bpj.2013.11.4469  0.56
2013 Pufall MA, Kaplan CD. Mechanisms of eukaryotic transcription. Genome Biology. 14: 311. PMID 24079829 DOI: 10.1186/Gb-2013-14-9-311  0.46
2013 Viktorovskaya OV, Engel KL, French SL, Cui P, Vandeventer PJ, Pavlovic EM, Beyer AL, Kaplan CD, Schneider DA. Divergent contributions of conserved active site residues to transcription by eukaryotic RNA polymerases I and II. Cell Reports. 4: 974-84. PMID 23994471 DOI: 10.1016/J.Celrep.2013.07.044  0.51
2013 Braberg H, Jin H, Moehle EA, Chan YA, Wang S, Shales M, Benschop JJ, Morris JH, Qiu C, Hu F, Tang LK, Fraser JS, Holstege FC, Hieter P, Guthrie C, ... Kaplan CD, et al. From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell. 154: 775-88. PMID 23932120 DOI: 10.1016/J.Cell.2013.07.033  0.515
2013 Kaplan CD. Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae Biochimica Et Biophysica Acta - Gene Regulatory Mechanisms. 1829: 39-54. PMID 23022618 DOI: 10.1016/J.Bbagrm.2012.09.007  0.632
2012 Kaplan CD, Jin H, Zhang IL, Belyanin A. Dissection of Pol II Trigger Loop function and Pol II activity-dependent control of start site selection in vivo Plos Genetics. 8. PMID 22511879 DOI: 10.1371/Journal.Pgen.1002627  0.555
2012 Larson MH, Zhou J, Kaplan CD, Palangat M, Kornberg RD, Landick R, Block SM. Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II. Proceedings of the National Academy of Sciences of the United States of America. 109: 6555-60. PMID 22493230 DOI: 10.1073/Pnas.1200939109  0.597
2012 Murakami K, Gibbons BJ, Davis RE, Nagai S, Liu X, Robinson PJ, Wu T, Kaplan CD, Kornberg RD. Tfb6, a previously unidentified subunit of the general transcription factor TFIIH, facilitates dissociation of Ssl2 helicase after transcription initiation. Proceedings of the National Academy of Sciences of the United States of America. 109: 4816-21. PMID 22411836 DOI: 10.1073/Pnas.1201448109  0.526
2012 Zhou J, Larson MH, Kaplan C, Palangat M, Kornberg RD, Landick R, Block SM. RNA Polymerase II Translocation and Fidelity are Governed by Trigger Loop Dynamics: A Single-Molecule Study Biophysical Journal. 102: 285a. DOI: 10.1016/J.Bpj.2011.11.1576  0.547
2011 Hartzog GA, Kaplan CD. Competing for the clamp: promoting RNA polymerase processivity and managing the transition from initiation to elongation. Molecular Cell. 43: 161-3. PMID 21777806 DOI: 10.1016/J.Molcel.2011.07.002  0.557
2010 Suh MH, Meyer PA, Gu M, Ye P, Zhang M, Kaplan CD, Lima CD, Fu J. A dual interface determines the recognition of RNA polymerase II by RNA capping enzyme. The Journal of Biological Chemistry. 285: 34027-38. PMID 20720002 DOI: 10.1074/Jbc.M110.145110  0.528
2010 Kaplan CD. The architecture of RNA polymerase fidelity Bmc Biology. 8. PMID 20598112 DOI: 10.1186/1741-7007-8-85  0.507
2009 Kaplan CD, Kaplan J. Iron acquisition and transcriptional regulation. Chemical Reviews. 109: 4536-52. PMID 19705827 DOI: 10.1021/Cr9001676  0.365
2009 Taft RJ, Kaplan CD, Simons C, Mattick JS. Evolution, biogenesis and function of promoter-associated RNAs. Cell Cycle (Georgetown, Tex.). 8: 2332-8. PMID 19597344 DOI: 10.4161/Cc.8.15.9154  0.594
2009 Kaplan CD. Revealing the hidden relationship between nucleosomes and splicing Cell Cycle. 8: 3631-3635. DOI: 10.4161/Cc.8.22.10289  0.305
2008 Kaplan CD, Kornberg RD. A bridge to transcription by RNA polymerase. Journal of Biology. 7: 39. PMID 19090964 DOI: 10.1186/Jbiol99  0.544
2008 Kaplan CD, Larsson KM, Kornberg RD. The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. Molecular Cell. 30: 547-56. PMID 18538653 DOI: 10.1016/J.Molcel.2008.04.023  0.429
2007 Bucheli ME, He X, Kaplan CD, Moore CL, Buratowski S. Polyadenylation site choice in yeast is affected by competition between Npl3 and polyadenylation factor CFI. Rna (New York, N.Y.). 13: 1756-64. PMID 17684230 DOI: 10.1261/Rna.607207  0.544
2007 Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD. Structural basis of RNA polymerase II substrate specificity and catalysis The Faseb Journal. 21. DOI: 10.1096/Fasebj.21.5.A656-C  0.485
2006 Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell. 127: 941-54. PMID 17129781 DOI: 10.1016/J.Cell.2006.11.023  0.568
2005 Kaplan CD, Holland MJ, Winston F. Interaction between transcription elongation factors and mRNA 3'-end formation at the Saccharomyces cerevisiae GAL10-GAL7 locus. The Journal of Biological Chemistry. 280: 913-22. PMID 15531585 DOI: 10.1074/Jbc.M411108200  0.687
2003 Kaplan CD, Laprade L, Winston F. Transcription elongation factors repress transcription initiation from cryptic sites. Science (New York, N.Y.). 301: 1096-9. PMID 12934008 DOI: 10.1126/Science.1087374  0.668
2000 Kaplan CD, Morris JR, Wu C, Winston F. Spt5 and spt6 are associated with active transcription and have characteristics of general elongation factors in D. melanogaster. Genes & Development. 14: 2623-34. PMID 11040216 DOI: 10.1101/Gad.831900  0.668
2000 Dixon DA, Kaplan CD, McIntyre TM, Zimmerman GA, Prescott SM. Post-transcriptional control of cyclooxygenase-2 gene expression. The role of the 3'-untranslated region. The Journal of Biological Chemistry. 275: 11750-7. PMID 10766797 DOI: 10.1074/Jbc.275.16.11750  0.415
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