Publications

Max Planck Institute for Multidisciplinary Sciences

Journal Article (327)

51.

Journal Article

Xiong, L.; Tolen, E. A.; Choi, J.; Velychko, S.; Caizzi, L.; Velychko, T.; Adachi, K.; MacCarthy, C. M.; Lidschreiber, M.; Cramer, P. et al.; Schöler, H. R.: Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells. eLife 11, e71533 (2022)

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52.

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Dombrowski, M.; Engeholm, M.; Dienemann, C.; Dodonova, S. O.; Cramer, P.: Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory. Nature Structural & Molecular Biology 29 (5), pp. 493 - 501 (2022)

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53.

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Sahu, B.; Hartonen, T.; Pihlajamaa, P.; Wei, B.; Dave, K.; Zhu, F.; Kaasinen, E.; Lidschreiber, K.; Lidschreiber, M.; Daub, C. O. et al.; Cramer, P.; Kivioja, T.; Taipale, J.: Sequence determinants of human gene regulatory elements. Nature Genetics 54 (3), pp. 283 - 294 (2022)

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54.

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Downes, D. J.; Smith, A. L.; Karpinska, M. A.; Velychko, T.; Rue-Albrecht, K.; Sims, D.; Milne, T. A.; Davies, J. O. J.; Oudelaar, A. M.; Hughes, J. R.: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nature Protocols 17 (2), pp. 445 - 475 (2022)

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55.

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Baar, T.; Dümcke, S.; Gressel, S.; Schwalb, B.; Dilthey, A.; Cramer, P.; Tresch, A.: RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history. G3: Genes, Genomes, Genetics 12 (5), jkac054 (2022)

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56.

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Shao, R.; Kumar, B.; Lidschreiber, K.; Lidschreiber, M.; Cramer, P.; Elsässer, S. J.: Distinct transcription kinetics of pluripotent cell states. Molecular Systems Biology 18 (1), e10407 (2022)

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57.

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Fianu, I.; Chen, Y.; Dienemann, C.; Dybkov, O.; Linden, A.; Urlaub, H.; Cramer, P.: Structural basis of Integrator-mediated transcription regulation. Science 374 (6569), pp. 883 - 887 (2021)

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58.

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Kokic, G.; Wagner, F. R.; Chernev, A.; Urlaub, H.; Cramer, P.: Structural basis of human transcription–DNA repair coupling. Nature 598 (7880), pp. 368 - 372 (2021)

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59.

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Aibara, S.; Dienemann, C.; Cramer, P.: Structure of an inactive RNA polymerase II dimer. Nucleic Acids Research 49 (18), pp. 10747 - 10755 (2021)

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60.

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García-Martínez, J.; Medina, D. A.; Bellvís, P.; Sun, M.; Cramer, P.; Chávez, S.; Pérez-Ortín, J. E.: The total mRNA concentration buffering system in yeast is global rather than gene-specific. RNA 27 (10), pp. 1281 - 1290 (2021)

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61.

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Güttler, T.; Aksu, M.; Dickmanns, A.; Stegmann, K. M.; Gregor, K.; Rees, R.; Taxer, W.; Rymarenko, O.; Schünemann, J.; Dienemann, C. et al.; Gunkel, P.; Mussil, B.; Krull, J.; Teichmann, U.; Groß, U.; Cordes, V.; Dobbelstein, M.; Görlich, D.: Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies. EMBO Journal 40 (19), e107985 (2021)

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62.

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Bhatta, A.; Dienemann, C.; Cramer, P.; Hillen, H.: Structural basis of RNA processing by human mitochondrial RNase P. Nature Structural and Molecular Biology 28 (9), pp. 713 - 723 (2021)

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63.

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Cramer, P.: AlphaFold2 and the future of structural biology. Nature Structural and Molecular Biology 28 (9), pp. 704 - 705 (2021)

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64.

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Kabinger, F.; Stiller, C.; Schmitzova, J.; Dienemann, C.; Kokic, G.; Hillen, H. S.; Höbartner, C.; Cramer, P.: Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis. Nature Structural and Molecular Biology 28 (9), pp. 740 - 746 (2021)

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65.

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Jochheim, F. A.; Tegunov, D.; Hillen, H. S.; Schmitzova, J.; Kokic, G.; Dienemann, C.; Cramer, P.: The structure of a dimeric form of SARS-CoV-2 polymerase. Communications Biology 4, 999 (2021)

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66.

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Zumer, K.; Maier, K. C.; Farnung, L.; Jaeger, M. G.; Rus, P.; Winter, G.; Cramer, P.: Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo. Molecular Cell 81 (15), pp. 3096 - 3109.e8 (2021)

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67.

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Wang, H.; Xiong, L.; Cramer, P.: Structures and implications of TBP–nucleosome complexes. Proceedings of the National Academy of Sciences of the USA 118 (30), e2108859118 (2021)

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68.

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Schilbach, S.; Aibara, S.; Dienemann, C.; Grabbe, F.; Cramer, P.: Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening. Cell 184 (15), pp. 4064 - 4072.e28 (2021)

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69.

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Chen, Y.; Vos, S. M.; Dienemann, C.; Ninov, M.; Urlaub, H.; Cramer, P.: Allosteric transcription stimulation by RNA polymerase II super elongation complex. Molecular Cell 81 (16), pp. 3386 - 3399.e10 (2021)

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70.

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Aibara, S.; Schilbach, S.; Cramer, P.: Structures of mammalian RNA polymerase II pre-initiation complexes. Nature 594 (7861), pp. 124 - 128 (2021)

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71.

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Rengachari, S.; Schilbach, S.; Aibara, S.; Dienemann, C.; Cramer, P.: Structure of the human Mediator-RNA polymerase II pre-initiation complex. Nature 594 (7861), pp. 129 - 133 (2021)

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72.

Journal Article

Osman, S.; Mohammad, E.; Lidschreiber, M.; Stuetzer, A.; Bazsó, F. L.; Maier, K. C.; Urlaub, H.; Cramer, P.: The Cdk8 kinase module regulates interaction of the mediator complex with RNA polymerase II. Journal of Biological Chemistry 296, 100734 (2021)

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73.

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Oberbeckmann, E.; Niebauer, V.; Watanabe, S.; Farnung, L.; Moldt, M.; Schmid, A.; Cramer, P.; Peterson, C. L.; Eustermann, S.; Hopfner, K.-P. et al.; Korber, P.: Ruler elements in chromatin remodelers set nucleosome array spacing and phasing. Nature Communications 12, 3232 (2021)

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74.

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Fianu, I.; Dienemann, C.; Aibara, S.; Schilbach, S.; Cramer, P.: Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2. Communications Biology 4, 606 (2021)

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75.

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Caizzi, L.; Monteiro-Martins, S.; Schwalb, B.; Lysakovskaya, K.; Schmitzova, J.; Sawicka, A.; Chen, Y.; Lidschreiber, M.; Cramer, P.: Efficient RNA polymerase II pause release requires U2 snRNP function. Molecular Cell 81 (9), pp. 1920 - 1934.e9 (2021)

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76.

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Hillen, H. S.; Markov, D. A.; Wojtas, I. D.; Hofmann, K. B.; Lidschreiber, M.; Cowan, A. T.; Jones, J. L.; Temiakov, D.; Cramer, P.; Anikin, M.: The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3′-UTRs of yeast mitochondrial mRNAs. Proceedings of the National Academy of Sciences of the USA 118 (15), e2009329118 (2021)

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77.

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Farnung, L.; Ochmann, M.; Engeholm, M.; Cramer, P.: Structural basis of nucleosome transcription mediated by Chd1 and FACT. Nature Structural and Molecular Biology 28 (4), pp. 382 - 387 (2021)

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78.

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Choi, J.; Lysakovskaia, K.; Stik, G.; Demel, C.; Söding, J.; Tian, T. V.; Graf, T.; Cramer, P.: Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. eLife 10, e65381 (2021)

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79.

Journal Article

Rawat, P.; Böhning, M.; Hummel, B.; Aprile-Garcia, F.; Pandit, A. S.; Eisenhardt, N.; Khavaran, A.; Niskanen, E.; Vos, S. M.; Palvimo, J. J. et al.; Pichler, A.; Cramer, P.; Sawarkar, R.: Stress-induced nuclear condensation of NELF drives transcriptional downregulation. Molecular Cell 81 (5), pp. 1013 - 1026.e11 (2021)

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80.

Journal Article

Endres, T.; Solvie, D.; Heidelberger, J. B.; Andriolett, V.; Baluapuri, A.; Ade, C. P.; Muhar, M.; Eilers, U.; Vos, S. M.; Cramer, P. et al.; Zuber, J.; Beli, P.; Popov, N.; Wolf, E.; Gallant, P.; Eilers, M.: Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters. Molecular Cell 81 (4), pp. 830 - 844.e13 (2021)

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81.

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Sawicka, A.; Villamil, G.; Lidschreiber, M.; Darzacq, X.; Dugast‐Darzacq, C.; Schwalb, B.; Cramer, P.: Transcription activation depends on the length of the RNA polymerase II C‐terminal domain. EMBO Journal 40 (9), e107015 (2021)

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82.

Journal Article

Tegunov, D.; Xue, L.; Dienemann, C.; Cramer, P.; Mahamid, J.: Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells. Nature Methods 18 (2), pp. 186 - 193 (2021)

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83.

Journal Article

Zhang, S.; Aibara, S.; Vos, S. M.; Agafonov, D.; Lührmann, R.; Cramer, P.: Structure of a transcribing RNA polymerase II–U1 snRNP complex. Science 371 (6526), pp. 305 - 309 (2021)

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supplementary-material

84.

Journal Article

Kokic, G.; Hillen, H. S.; Tegunov, D.; Dienemann, C.; Seitz, F.; Schmitzova, J.; Farnung, L.; Siewert, A.; Höbartner, C.; Cramer, P.: Mechanism of SARS-CoV-2 polymerase stalling by remdesivir. Nature Communications 12, 279 (2021)

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85.

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Kokic, G.; Hillen, H. S.; Tegunov, D.; Dienemann, C.; Seitz, F.; Schmitzova, J.; Farnung, L.; Siewert, A.; Höbartner, C.; Cramer, P.: Mechanism of SARS-CoV-2 polymerase stalling by remdesivir. Nature Communications 12, 279 (2021)

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86.

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Cramer, P.; Kokic, G.; Dienemann, C.; Höbartner, C.; Hillen, H. S.: Coronavirus-Replikation: Mechanismus und Inhibition durch Remdesivir. Biospektrum 27 (1), pp. 49 - 53 (2021)

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87.

Journal Article

Kim, K.-P.; Choi, J.; Yoon, J.; Bruder, J. M.; Shin, B.; Kim, J.; Arauzo-Bravo, M. J.; Han, D.; Wu, G.; Han, D. W. et al.; Kim, J.; Cramer, P.; Schöler, H. R.: Permissive epigenomes endow reprogramming competence to transcriptional regulators. Nature Chemical Biology 17 (1), pp. 47 - 56 (2021)

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88.

Journal Article

Lidschreiber, K.; Jung, L. A.; von der Emd, H.; von der Emde, H.; Dave, K.; Taipale, J.; Cramer, P.; Lidschreiber, M.: Transcriptionally active enhancers in human cancer cells. Molecular Systems Biology 17 (1), e9873 (2021)

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89.

Journal Article

Lykke-Andersen, S.; Zumer, K.; Molska, E. Š.; Rouvière, J. O.; Wu, G.; Demel, C.; Schwalb, B.; Schmid, M.; Cramer, P.; Jensen, T. H.: Integrator is a genome-wide attenuator of non-productive transcription. Molecular Cell, in Press (2020)

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90.

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Bonekamp, N. A.; Peter, B.; Hillen, H. S.; Felser, A.; Bergbrede, T.; Choidas, A.; Horn, M.; Unger, A.; Di Lucrezia, R.; Atanassov, I. et al.; Li, X.; Koch, U.; Menninger, S.; Boros, J.; Habenberger, P.; Giavalisco, P.; Cramer, P.; Denzel, M. S.; Nussbaumer, P.; Klebl, B.; Falkenberg, M.; Gustafsson, C. M.; Larsson, N.-G.: Small-molecule inhibitors of human mitochondrial DNA transcription. Nature 588 (7839), pp. 712 - 716 (2020)

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91.

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Osman, S.; Cramer, P.: Structural biology of RNA polymerase II transcription: 20 years on. Annual Review of Cell and Developmental Biology 36, pp. 1 - 34 (2020)

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92.

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Maier, K. C.; Gressel, S.; Cramer, P.; Schwalb, B.: Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms. Genome Research 30 (9), pp. 1332 - 1344 (2020)

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93.

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Cramer, P.: Rosalind Franklin and the advent of molecular biology. Cell 182 (4), pp. 787 - 789 (2020)

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94.

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Tellier, M.; Zaborowska, J.; Caizzi, L.; Mohammad, E.; Velychko, T.; Schwalb, B.; Ferrer-Vicens, I.; Blears, D.; Nojima, T.; Cramer, P. et al.; Murphy, S.: CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation. Nucleic Acids Research 48 (14), pp. 7712 - 7727 (2020)

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95.

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Hillen, H.; Kokic, G.; Farnung, L.; Dienemann, C.; Tegunov, D.; Cramer, P.: Structure of replicating SARS-CoV-2 polymerase. Nature 584 (7819), pp. 154 - 156 (2020)

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96.

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O’Reilly, F. J.; Xue, L.; Graziadei, A.; Sinn, L.; Lenz, S.; Tegunov, D.; Blötz, C.; Singh, N.; Hagen, W. J. H.; Cramer, P. et al.; Stülke, J.; Mahamid, J.; Rappsilber, J.: In-cell architecture of an actively transcribing-translating expressome. Science 369 (6503), pp. 554 - 557 (2020)

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97.

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Jaeger, M. G.; Schwalb, B.; Mackowiak, S. D.; Velychko, T.; Hanzl, A.; Imrichova, H.; Brand, M.; Agerer, B.; Chorn, S.; Nabet, B. et al.; Ferguson, F. M.; Müller, A. C.; Bergthaler, A.; Gray, N. S.; Bradner, J. E.; Bock, C.; Hnisz, D.; Cramer, P.; Winter, G. E.: Selective Mediator dependence of cell-type-specifying transcription. Nature Genetics 52 (7), pp. 719 - 727 (2020)

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98.

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Stik, G.; Vidal, E.; Barrero, M.; Cuartero, S.; Vila-Casadesús, M.; Mendieta-Esteban, J.; Tian, T. V.; Choi, J.; Berenguer, C.; Abad, A. et al.; Borsari, B.; le Dily, F.; Cramer, P.; Marti-Renom, M. A.; Stadhouders, R.; Graf, T.: CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response. Nature Genetics 52 (7), pp. 655 - 661 (2020)

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99.

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Vos, S. M.; Farnung, L.; Linden, A.; Urlaub, H.; Cramer, P.: Structure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation. Nature Structural and Molecular Biology 27 (7), pp. 668 - 677 (2020)

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100.

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Farnung, L.; Ochmann, M.; Cramer, P.: Nucleosome-CHD4 chromatin remodeller structure maps human disease mutations. eLife 9, e56178 (2020)

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