Publikationen

Zeitschriftenartikel (209)

  1. MPG.PuRe
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    Hendriks, G. J.; Jung, L. A.; Larsson, A. J. M.; Lidschreiber, M.; Forsman, O. A.; Lidschreiber, K.; Cramer, P.; Sandberg, R.: NASC-seq monitors RNA synthesis in single cells. Nature Communications 10 (1) (2019)
  2. MPG.PuRe
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    Chen, Y.; Cramer, P.: Structure of the super-elongation complex subunit AFF4 C-terminal homology domain reveals requirements for AFF homo- and heterodimerization. Journal of Biological Chemistry 294, S. 10663 - 10673 (2019)
  3. MPG.PuRe
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    Kokic, G.; Chernev, A.; Tegunov, D.; Dienemann, C.; Urlaub, H.; Cramer, P.: Structural basis of TFIIH activation for nucleotide excision repair. Nature Communications 10 (2019)
  4. MPG.PuRe
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    Sohrabi-Jahromi, S.; Hofmann, K. B.; Boltendahl, A.; Roth, C.; Gressel, S.; Baejen, C.; Söding, J.; Cramer, P.: Transcriptome maps of general eukaryotic RNA degradation factors. eLife 8 (2019)
  5. MPG.PuRe
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    Baluapuri, A.; Hofstetter, J.; Dudvarski Stankovic, N.; Endres, T.; Bhandare, P.; Vos, S. M.; Adhikari, B.; Schwarz, J. D.; Narain, A.; Vogt, M. et al.; Wang, S. Y.; Düster, R.; Jung, L. A.; Vanselow, J. T.; Wiegering, A.; Geyer, M.; Maric, H. M.; Gallant, P.; Walz, S.; Schlosser, A.; Cramer, P.; Eilers, M.; Wolf, E.: MYC recruits SPT5 to RNA polymerase II to promote processive transcription elongation. Molecular Cell 74 (4), S. 674 - 687 (2019)
  6. MPG.PuRe
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    Dodonova, S. O.; Prinz, S.; Bilanchone, V.; Sandmeyer, S.; Briggs, J. A. G.: Structure of the Ty3/Gypsy retrotransposon capsid and the evolution of retroviruses. Proceedings of the National Academy of Sciences of the United States of America 116 (20) (2019)
  7. MPG.PuRe
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    Wachutka, L.; Caizzi, L.; Gagneur, J.; Cramer, P.: Global donor and acceptor splicing site kinetics in human cells. eLife 8 (2019)
  8. MPG.PuRe
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    Jones, J. L.; Hofmann, K. B.; Cowan, A. T.; Temiakov, D.; Cramer, P.; Anikin, M.: Yeast mitochondrial protein Pet111p binds directly to two distinct targets in COX2 mRNA, suggesting a mechanism of translational activation. Journal of Biological Chemistry (2019)
  9. MPG.PuRe
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    Villamizar, G. A. C.; Nacke, H.; Böhning, M.; Herz, K.; Daniel, R.: Functional metagenomics reveals an overlooked diversity and novel features of soil-derived bacterial phosphatases and phytases. mBio 10 (1), e01966-18 (2019)
  10. MPG.PuRe
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    Zylicz, J. J.; Bousard, A.; Zumer, K.; Dossin, F.; Mohammad, E.; da Rocha, S. T.; Schwalb, B.; Syx, L.; Dingli, F.; Loew, D. et al.; Cramer, P.; Heard, E.: The implication of early chromatin changes in X chromosome inactivation. Cell 176 (1-2), S. 182 - 197 (2019)
  11. MPG.PuRe
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    Dienemann, C.; Schwalb, B.; Schilbach, S.; Cramer, P.: Promoter distortion and opening in the RNA polymerase II cleft. Molecular Cell 73 (1), S. 97 - 106 (2019)
  12. MPG.PuRe
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    Farnung, L.; Vos, S. M.; Cramer, P.: Structure of transcribing RNA polymerase II-nucleosome complex. Nature Communications 9 (2018)
  13. MPG.PuRe
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    Lidschreiber, M.; Easter, A. D.; Battaglia, S.; Rodríguez-Molina, J. B.; Casañal, A.; Carminati, M.; Baejen, C.; Grzechnik, P.; Maier, K. C.; Cramer, P. et al.; Passmore, L. A.: The APT complex is involved in non-coding RNA transcription and is distinct from CPF. Nucleic Acids Research 46 (21), S. 11528 - 11538 (2018)
  14. MPG.PuRe
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    Ortega, E.; Rengachari, S.; Ibrahim, Z.; Hoghoughi, N.; Gaucher, J.; Holehouse, A. S.; Khochbin, S.; Panne, D.: Transcription factor dimerization activates the p300 acetyltransferase. Nature 562 (7728), S. 538 - 544 (2018)
  15. MPG.PuRe
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    Zhu, F.; Farnung, L.; Kaasinen, E.; Sahu, B.; Yin, Y.; Wei, B.; Dodonova, S. O.; Nitta, K. R.; Morgunova, E.; Taipale, M. et al.; Cramer, P.; Taipale, J.: The interaction landscape between transcription factors and the nucleosome. Nature 562 (7725), S. 76 - 81 (2018)
  16. MPG.PuRe
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    Böhning, M.; Dugast-Darzacq, C.; Rankovic, M.; Hansen, A. S.; Yu, T.; Marie-Nelly, H.; McSwiggen, D. T.; Kokic, G.; Dailey, G. M.; Cramer, P. et al.; Darzacq, X.; Zweckstetter, M.: RNA polymerase II clustering through carboxy-terminal domain phase separation. Nature Structural and Molecular Biology 25 (9), S. 833 - 840 (2018)
  17. MPG.PuRe
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    Hillen, H. S.; Temiakov, D.; Cramer, P.: Structural basis of mitochondrial transcription. Nature Structural and Molecular Biology 25 (9), S. 754 - 765 (2018)
  18. MPG.PuRe
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    Vos, S. M.; Farnung, L.; Urlaub, H.; Cramer, P.: Structure of paused transcription complex Pol II–DSIF–NELF. Nature 560 (7720), S. 601 - 606 (2018)
  19. MPG.PuRe
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    Vos, S. M.; Farnung, L.; Böhning, M.; Wigge, C.; Linden, A.; Urlaub, H.; Cramer, P.: Structure of activated transcription complex Pol II-DSIF-PAF-SPT6. Nature 560 (7720), S. 607 - 612 (2018)
  20. MPG.PuRe
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    La Manno, G.; Soldatov, R.; Zeisel, A.; Braun, E.; Hochgerner, H.; Petukhov, V.; Lidschreiber, K.; Kastriti, M. E.; Lönnerberg, P.; Furlan, A. et al.; Fan, J.; Borm, L. E.; Liu, Z.; van Bruggen, D.; Guo, J.; He, X.; Barker, R.; Sundström, E.; Castelo-Branco, G.; Cramer, P.; Adameyko, I.; Linnarsson, S.; Kharchenko, P. V.: RNA velocity of single cells. Nature 560 (7719), S. 494 - 498 (2018)
  21. MPG.PuRe
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    Liu, X.; Farnung, L.; Wigge, C.; Cramer, P.: Cryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by α-amanitin. Journal of Biological Chemistry 293 (19), S. 7189 - 7194 (2018)
  22. MPG.PuRe
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    Engel, C.; Neyer, S.; Cramer, P.: Distinct mechanisms of transcription initiation by RNA polymerases I and II. Annual Review of Biophysics 47, S. 425 - 446 (2018)
  23. MPG.PuRe
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    Hantsche, M.; Cramer, P.: Conserved RNA polymerase II initiation complex structure. Current Opinion in Structural Biology 47, S. 17 - 22 (2017)
  24. MPG.PuRe
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    Bykov, Y. S.; Schaffer, M.; Dodonova, S. O.; Albert, S.; Plitzko, J. M.; Baumeister, W.; Engel, B. D.; Briggs, J. A. G.: The structure of the COPI coat determined within the cell. eLife 6 (2017)
  25. MPG.PuRe
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    Hillen, H. S.; Parshin, A. V.; Agaronyan, K.; Morozov, Y. I.; Graber, J. J.; Chernev, A.; Schwinghammer, K.; Urlaub, H.; Anikin, M.; Cramer, P. et al.; Temiakov, D.: Mechanism of transcription anti-termination in human mitochondria. Cell 171 (5), S. 1082 - 1093 (2017)
  26. MPG.PuRe
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    Hillen, H. S.; Morozov, Y. I.; Sarfallah, A.; Temiakov, D.; Cramer, P.: Structural basis of mitochondrial transcription initiation. Cell 171 (5), S. 1072 - 1081 (2017)
  27. MPG.PuRe
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    Malvezzi, S.; Farnung, L.; Aloisi, C. M. N.; Angelov, T.; Cramer, P.; Sturla, S. J.: Mechanism of RNA polymerase II stalling by DNA alkylation. Proceedings of the National Academy of Sciences of the United States of America 114 (46), S. 12172 - 12177 (2017)
  28. MPG.PuRe
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    Schilbach, S.; Hantsche, M.; Tegunov, D.; Dienemann, C.; Wigge, C.; Urlaub, H.; Cramer, P.: Structures of transcription pre-initiation complex with TFIIH and Mediator. Nature 551 (7679), S. 204 - 209 (2017)
  29. MPG.PuRe
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    Cheng, J.; Maier, K. C.; Avsec, Z.; Rus, P.; Gagneur, J.: Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast. RNA 23 (11), S. 1648 - 1659 (2017)
  30. MPG.PuRe
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    Farnung, L.; Vos, S. M.; Wigge, C.; Cramer, P.: Nucleosome-Chd1 structure and implications for chromatin remodelling. Nature 550 (7677), S. 539 - 542 (2017)
  31. MPG.PuRe
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    Gressel, S.; Schwalb, B.; Decker, T. M.; Qin, W.; Leonhardt, H.; Eick, D.; Cramer, P.: CDK9-dependent RNA polymerase II pausing controls transcription initiation. eLife 6 (2017)
  32. MPG.PuRe
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    Bernecky, C.; Plitzko, J. M.; Cramer, P.: Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nature Structural and Molecular Biology 24 (10), S. 809 - 815 (2017)
  33. MPG.PuRe
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    Glaser, L. V.; Rieger, S.; Thumann, S.; Beer, S.; Kuklik-Roos, C.; Martin, D. E.; Maier, K. C.; Harth-Hertle, M. L.; Grüning, B.; Backofen, R. et al.; Krebs, S.; Blum, H.; Zimmer, R.; Erhard, F.; Kempkes, B.: EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells. PLoS Pathogens 13 (10), e1006664 (2017)
  34. MPG.PuRe
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    Cramer, P.: Structural molecular biology - A personal reflection on the occasion of John Kendrew's 100th birthday. Journal of Molecular Biology 429 (17), S. 2603 - 2610 (2017)
  35. MPG.PuRe
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    Boratyn, E.; Nowak, I.; Durbas, M.; Horwacik, I.; Sawicka, A.; Rokita, H.: MCPIP1 exogenous overexpression inhibits pathways regulating MYCN oncoprotein stability in neuroblastoma. Journal of Cellular Biochemistry 118 (7), S. 1741 - 1755 (2017)
  36. MPG.PuRe
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    Dodonova, S. O.; Aderhold, P.; Kopp, J.; Ganeva, I.; Röhling, S.; Hagen, W. J. H.; Sinning, I.; Wieland, F.; Briggs, J. A. G.: 9 angstrom structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments. eLife 6 (2017)
  37. MPG.PuRe
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    Xu, Y.; Bernecky, C.; Lee, C. T.; Maier, K. C.; Schwalb, B.; Tegunov, D.; Plitzko, J. M.; Urlaub, H.; Cramer, P.: Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications 8 (2017)
  38. MPG.PuRe
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    Battaglia, S.; Lidschreiber, M.; Bäjen, C.; Torkler, P.; Vos, S. M.; Cramer, P.: RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases. eLife 6 (2017)
  39. MPG.PuRe
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    Nozawa, K.; Schneider, T. R.; Cramer, P.: Core Mediator structure at 3.4 Å extends model of transcription initiation complex. Nature 545 (7653), S. 248 - 251 (2017)
  40. MPG.PuRe
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    Kohler, R.; Mooney, R. A.; Mills, D. J.; Landick, R.; Cramer, P.: Architecture of a transcribing-translating expressome. Science 356 (6334), S. 194 - 197 (2017)
  41. MPG.PuRe
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    Bäjen, C.; Andreani, J.; Torkler, P.; Battaglia, S.; Schwalb, B.; Lidschreiber, M.; Maier, K. C.; Boltendahl, A.; Rus, P.; Esslinger, S. et al.; Söding, J.; Cramer, P.: Genome-wide analysis of RNA polymerase II termination at protein-coding genes. Molecular Cell 66 (1), S. 38 - 49 (2017)
  42. MPG.PuRe
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    Shetty, A.; Kallgren, S. P.; Demel, C.; Maier, K. C.; Spatt, D.; Alver, B. H.; Cramer, P.; Park, P. J.; Winston, F.: Spt5 plays vital roles in the control of sense and antisense transcription elongation. Molecular Cell 66 (6), S. 77 - 88 (2017)
  43. MPG.PuRe
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    Wittmann, S.; Renner, M.; Watts, B. R.; Adams, O.; Huseyin, M.; Baejen, C.; El Omari, K.; Kilchert, C.; Heo, D. H.; Kecman, T. et al.; Cramer, P.; Grimes, J. M.; Vasiljeva, L.: The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA. Nature Communications 8 (2017)
  44. MPG.PuRe
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    Engel, C.; Gubbey, T.; Neyer, S.; Sainsbury, S.; Oberthür, C.; Bäjen, C.; Bernecky, C.; Cramer, P.: Structural basis of RNA polymerase I transcription initiation. Cell 169 (1), S. 120 - 131 (2017)
  45. MPG.PuRe
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    Michel, M.; Demel, C.; Zacher, B.; Schwalb, B.; Krebs, S.; Blum, H.; Gagneur, J.; Cramer, P.: TT-seq captures enhancer landscapes immediately after T-cell stimulation. Molecular Systems Biology 13 (3) (2017)
  46. MPG.PuRe
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    Danev , R.; Tegunov, D.; Baumeister, W.: Using the Volta phase plate with defocus for cryo-EM single particle analysis. eLife 6 (2017)
  47. MPG.PuRe
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    Zacher, B.; Michel, M.; Schwalb, B.; Cramer, P.; Tresch, A.; Gagneur, J.: Accurate promoter and enhancer identification in 127 ENCODE and roadmap epigenomics cell types and tissues by GenoSTAN. PLoS One 12 (1) (2017)
  48. MPG.PuRe
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    Hantsche, M.; Cramer, P.: Structural basis of transcription: 10 years after the Nobel Prize in Chemistry. Angewandte Chemie International Edition 55 (52), S. 15972 - 15981 (2016)
  49. MPG.PuRe
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    Neyer, S.; Kunz, M.; Geiss, C.; Hantsche, M.; Hodirnau, V. V.; Seybert, A.; Engel, C.; Scheffer, M. P.; Cramer, P.; Frangakis, A. S.: Structure of RNA polymerase I transcribing ribosomal DNA genes. Nature 540 (7634), S. 607 - 610 (2016)
  50. MPG.PuRe
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    Fitz, V.; Shin, J.; Ehrlich, C.; Farnung, L.; Cramer, P.; Zaburdaev, V.; Grill, S. W.: Nucleosomal arrangement affects single-molecule transcription dynamics. Proceedings of the National Academy of Sciences of the United States of America 113 (45) (2016)
  51. MPG.PuRe
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    Hillenbrand, P.; Maier, K. C.; Cramer, P.; Gerland, U.: Inference of gene regulation functions from dynamic transcriptome data. eLife 5 (2016)
  52. MPG.PuRe
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    Shao, W.; Zumer, K.; Fujinaga, K.; Peterlin, B. M.: FBXO3 protein promotes ubiquitylation and transcriptional activity of AIRE (Autoimmune Regulator). Journal of Biological Chemistry 291 (34), S. 17953 - 17963 (2016)
  53. MPG.PuRe
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    Cramer, P.: Structure determination of transient transcription complexes. Biochemical Society Transactions 44 (4), S. 1177 - 1182 (2016)
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    Engel, C.; Plitzko, J.; Cramer, P.: RNA polymerase I-Rrn3 complex at 4.8 Å resolution. Nature Communications 7 (2016)
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    Plaschka, C.; Nozawa, K.; Cramer, P.: Mediator architecture and RNA polymerase II interaction. Journal of Molecular Biology 428 (12), S. 2569 - 2574 (2016)
  56. MPG.PuRe
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    Vos, S. M.; Pöllmann, D.; Caizzi, L.; Hofmann, K. B.; Rombaut, P.; Zimniak, T.; Herzog, F.; Cramer, P.: Architecture and RNA binding of the human negative elongation factor. eLife 5 (2016)
  57. MPG.PuRe
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    Schwalb, B.; Michel, M.; Zacher, B.; Frühauf, K.; Demel, C.; Tresch, A.; Gagneur, J.; Cramer, P.: TT-seq maps the human transient transcriptome. Science 352 (6290), S. 1225 - 1228 (2016)
  58. MPG.PuRe
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    Plaschka, C.; Hantsche, M.; Dienemann, C.; Burzinski, C.; Plitzko, J.; Cramer, P.: Transcription initiation complex structures elucidate DNA opening. Nature 533 (7603), S. 353 - 358 (2016)
  59. MPG.PuRe
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    Lisica, A.; Engel, C.; Jahnel, M.; Roldán, É.; Galburt, E. A.; Cramer, P.; Grill, S. W.: Mechanisms of backtrack recovery by RNA polymerases I and II. Proceedings of the National Academy of Sciences of the United States of America 113 (11) (2016)
  60. MPG.PuRe
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    Niesser, J.; Wagner, F. R.; Kostrewa, D.; Mühlbacher, W.; Cramer, P.: Structure of GPN-loop GTPase Npa3 and implications for RNA polymerase II assembly. Molecular and Cellular Biology 36 (5), S. 820 - 831 (2016)
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    Eser, P.; Wachutka, L.; Maier, K. C.; Demel, C.; Boroni, M.; Iyer, S.; Cramer, P.; Gagneur, J.: Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Molecular Systems Biology 12 (2) (2016)
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    Schüller, R.; Forné, I.; Straub, T.; Schreieck, A.; Texier, Y.; Shah, N.; Decker, T. M.; Cramer, P.; Imhof, A.; Eick, D.: Heptad-specific phosphorylation of RNA polymerase II CTD. Molecular Cell 61 (2), S. 305 - 314 (2016)
  63. MPG.PuRe
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    Mühlbacher, W.; Mayer, A.; Sun, M.; Remmert, M.; Cheung, A. C. M.; Niesser, J.; Söding, J.; Cramer, P.: Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a non-canonical CTD-interacting domain fold. Proteins: Structure, Function, and Bioinformatics 83 (10), S. 1849 - 1858 (2015)
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    Kostrewa, D.; Kuhn, C. D.; Engel, C.; Cramer, P.: An alternative RNA polymerase I structure reveals a dimer hinge. Acta Crystallographica D 71 (9) (2015)
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    Martinez-Rucobo, F. W.; Kohler, R.; Waterbeemd, M. v. d.; Heck, A. J.; Hemann, M.; Herzog, F.; Stark, H.; Cramer, P.: Molecular basis of transcription-coupled pre-mRNA capping. Molecular Cell 58 (6), S. 1079 - 1089 (2015)
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    Morozov, Y. I.; Parshin, A. V.; Agaronyan, K.; Cheung, A. C.; Anikin, M.; Cramer, P.; Temiakov, D.: A model for transcription initiation in human mitochondria. Nucleic Acids Research 43 (7) (2015)
  67. MPG.PuRe
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    Sainsbury, S.; Bernecky, C.; Cramer, P.: Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology 16 (3), S. 129 - 143 (2015)
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    Plaschka, C.; Larivière, L.; Wenzeck, L.; Seizl, M.; Hemann, M.; Tegunov, D.; Petrotchenko, E. V.; Borchers, C. H.; Baumeister, W.; Herzog, F. et al.; Villa, E.; Cramer, P.: Architecture of the RNA polymerase II–Mediator core initiation complex. Nature 518 (7539), S. 376 - 380 (2015)
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    Borck, G.; Hög, F.; Dentici, M. L.; Tan, P. L.; Sowada, N.; Medeira, A.; Gueneau, L.; Thiele, H.; Kousi, M.; Lepri, F. et al.; Wenzeck, L.; Blumenthal, I.; Radicioni, A.; Schwarzenberg, T. L.; Mandriani, B.; Fischetto, R.; Morris-Rosendahl, D. J.; Altmüller, J.; Reymond, A.; Nürnberg, P.; Merla, G.; Dallapiccola, B.; Katsanis, N.; Cramer, P.; Kubisch, C.: BRF1 mutations alter RNA polymerase III-dependent transcription and cause neurodevelopmental anomalies. Genome Research 25 (2), S. 155 - 166 (2015)
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    Zacher, B.; Lidschreiber, M.; Cramer, P.; Gagneur, J.; Tresch, A.: Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle. Molecular Systems Biology 10 (12) (2014)
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    Cramer, P.: A tale of chromatin and transcription in 100 structures. Cell 159 (5) (2014)
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    Bäjen, C.; Torkler, P.; Gressel, S.; Essig, K.; Söding, J.; Cramer, P.: Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition. Molecular Cell 55 (5), S. 745 - 757 (2014)
  73. MPG.PuRe
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    Tudek, A.; Porrua, O.; Kabzinski, T.; Lidschreiber, M.; Kubicek, K.; Fortova, A.; Lacroute, F.; Vanakova, S.; Cramer, P.; Stefl, R. et al.; Libri, D.: Molecular basis for coordinating transcription termination with noncoding RNA degradation. Molecular Cell 55 (3), S. 467 - 481 (2014)
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    Mühlbacher, W.; Sainsbury, S.; Hemann, M.; Hantsche, M.; Neyer, S.; Herzog, F.; Cramer, P.: Conserved architecture of the core RNA polymerase II initiation complex. Nature Communications 5 (2014)
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