Publications

van den Heuvel, D.; Rodríguez-Martínez, M.; van der Meer, P. J.; Nieto Moreno, N.; Park, J.; Kim, H.-S.; van Schie, J. J.M.; Wondergem, A. P.; D’Souza, A.; Yakoub, G. et al.; Herlihy, A. E.; Kashyap, K.; Boissière, T.; Walker, J.; Mitter, R.; Apelt, K.; de Lint, K.; Kirdök, I.; Ljungman, M.; Wolthuis, R. M.F.; Cramer, P.; Schärer, O. D.; Kokic, G.; Svejstrup, J. Q.; Luijsterburg, M. S.: STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair. Cell 187 (25), pp. 7107 - 7125.e25 (2024)

Jochheim, A.; Jochheim, F. A.; Kolodyazhnaya, A.; Morice, É.; Steinegger, M.; Söding, J.: Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs. Microbiome 12, 187 (2024)

Engeholm, M.; Roske, J. J.; Oberbeckmann, E.; Dienemann, C.; Lidschreiber, M.; Cramer, P.; Farnung, L.: Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT. Molecular Cell 84 (18), pp. 3423 - 3437.e8 (2024)

Patil, S.; Cremosnik, G.; Dötsch, L.; Flegel, J.; Schulte, B.; Maier, K. C.; Žumer, K.; Cramer, P.; Janning, P.; Sievers, S. et al.; Ziegler, S.; Waldmann, H.: The Pseudo-Natural Product Tafbromin Selectively Targets the TAF1 Bromodomain 2. Angewandte Chemie International Edition 63 (32), e202404645 (2024)

Velychko, T.; Mohammad, E.; Ferrer-Vicens, I.; Parfentev, I.; Werner, M.; Studniarek, C.; Schwalb, B.; Urlaub, H.; Murphy, S.; Cramer, P. et al.; Lidschreiber, M.: CDK7 kinase activity promotes RNA polymerase II promoter escape by facilitating initiation factor release. Molecular Cell 84 (12), pp. 2287 - 2303.e10 (2024)

Žumer, K.; Ochmann, M.; Aljahani, A.; Zheenbekova, A.; Devadas, A.; Maier, K. C.; Rus, P.; Neef, U.; Oudelaar, A. M.; Cramer, P.: FACT maintains chromatin architecture and thereby stimulates RNA polymerase II pausing during transcription in vivo. Molecular Cell 84 (11), pp. 2053 - 2069.e9 (2024)

Müller, J.M.; Moos, K.; Baar, T.; Maier, K. C.; Zumer, K.; Tresch, A.: Nuclear export is a limiting factor in eukaryotic mRNA metabolism. PLOS Computational Biology 20 (5), e1012059 (2024)

Ibáñez de Opakua, A.; Pantoja, C. F.; Cima-Omori, M.-S.; Dienemann, C.; Zweckstetter, M.: Impact of distinct FG nucleoporin repeats on Nup98 self-association. Nature Communications 15, 3797 (2024)

Fianu, I.; Ochmann, M.; Walshe, J. L.; Dybkov, O.; Cruz, J. N.; Urlaub, H.; Cramer, P.: Structural basis of Integrator-dependent RNA polymerase II termination. Nature 629, pp. 219 - 227 (2024)

Zhan, Y.; Grabbe, F.; Oberbeckmann, E.; Dienemann, C.; Cramer, P.: Three-step mechanism of promoter escape by RNA polymerase II. Molecular Cell 84 (9), pp. 1699 - 1710.e6 (2024)

Cramer, P.: Good reasons for structural biology. Nature Structural & Molecular Biology 31, pp. 393 - 394 (2024)

Kokic, G.; Yakoub, G.; van den Heuvel, D.; Wondergem, A. P.; van der Meer, P. J.; van der Weegen, Y.; Chernev, A.; Fianu, I.; Fokkens, T. J.; Lorenz, S. et al.; Urlaub, H.; Cramer, P.; Luijsterburg, M. S.: Structural basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair. Nature Structural & Molecular Biology 31, pp. 536 - 547 (2024)

Oberbeckmann, E.; Quililan, K.; Cramer, P.; Oudelaar, A. M.: In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization. Nature Genetics 56, pp. 483 - 492 (2024)

Frieg, B.; Han, M.; Giller, K.; Dienemann, C.; Riedel, D.; Becker, S.; Andreas, L. B.; Griesinger, C.; Schröder, G. F.: Cryo-EM structures of lipidic fibrils of amyloid-β (1-40). Nature Communications 15, 1297 (2024)

Düring, J.; Wolter, M.; Toplak, J. J.; Torres, C.; Dybkov, O.; Fokkens, T. J.; Bohnsack, K. E.; Urlaub, H.; Steinchen, W.; Dienemann, C. et al.; Lorenz, S.: Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1. Nature Structural & Molecular Biology 31, pp. 364 - 377 (2024)

Chaban, A.; Minakhin, L.; Goldobina, E.; Bae, B.; Hao, Y.; Borukhov, S.; Putzeys, L.; Boon, M.; Kabinger, F.; Lavigne, R. et al.; Makarova, K.S.; Koonin, E.V.; Nair, S.K.; Tagami, S.; Severinov, K.; Sokolova, M. L.: Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail. Nature Communications 15, 317 (2024)

MacCarthy, C. M.; Wu, G.; Malik, V.; Menuchin-Lasowski, Y.; Velychko, T.; Keshet, G.; Fan, R.; Bedzhov, I.; Church, G. M.; Jauch, R. et al.; Cojocaru, V.; Schoeler, H. R.; Velychko, S.: Highly cooperative chimeric super-SOX induces naive pluripotency across species. Cell Stem Cell 31 (1), e9, pp. 127 - 147 (2024)

Chen, Y.; Cramer, P.: RNA polymerase II elongation factors use conserved regulatory mechanisms. Current Opinion in Structural Biology 84, 102766 (2024)

Oberbeckmann, E.; Oudelaar, A. M.: Genome organization across scales: mechanistic insights from in vitro reconstitution studies. Biochemical Society Transactions 52 (2), pp. 793 - 802 (2024)

Welp, L. M.; Sachsenberg, T.; Wulf, A.; Chernev, A.; Horokhovskyi, Y.; Neumann, P.; Pašen, M.; Siraj, A.; Raabe, M.; Johannsson, S. et al.; Schmitzova, J.; Netz, E.; Pfeuffer, J.; He, Y.; Fritzemeier, K.; Delanghe, B.; Viner, R.; Vos, S. M.; Cramer, P.; Ficner, R.; Liepe, J.; Kohlbacher, O.; Urlaub, H.: Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid–protein interaction sites by mass spectrometry. bioRxiv (2024)