Publications

Welp, L. M.; Wulf, A.; Chernev, A.; Horokhovskyi, Y.; Moshkovskii, S.; Dybkov, O.; Neumann, P.; Pašen, M.; Siraj, A.; Raabe, M. et al.; Göthert, H.; Walshe, J.; Infante, D. A.; de A P Schwarzer, A.; Dickmanns, A.; Johannsson, S.; Schmitzová, J.; Wohlgemuth, I.; Netz, E.; He, Y.; Fritzemeier, K.; Delanghe, B.; Viner, R.; Vos, S.; Oberbeckmann, E.; Bohnsack, K.; Bohnsack, M.; Cramer, P.; Ficner, R.; Kohlbacher, O.; Liepe, J.; Sachsenberg, T.; Urlaub, H.: Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid–protein interaction sites by mass spectrometry. Nucleic Acids Research 53 (15), gkaf727 (2025)

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5.

Journal Article

Zheenbekova, A.; Walshe, J. L.; Ochmann, M.; Bäuerle, M.; Neef, U.; Maier, K. C.; Rus, P.; Yan, Y.; Urlaub, H.; Cramer, P. et al.; Žumer, K.: IWS1 positions downstream DNA to globally stimulate Pol II elongation. Nature Communications 16, 7747 (2025)

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6.

Journal Article

Cruz-Zaragoza, L. D.; Dahal, D.; Koschel, M.; Boshnakovska, A.; Zheenbekova, A.; Yilmaz, M.; Morgenstern, M.; Dohrke, J.-N.; Bender, J.; Valpadashi, A. et al.; Henningfeld, K. A.; Oeljeklaus, S.; Kremer, L. S.; Breuer, M.; Urbach, O.; Dennerlein, S.; Lidschreiber, M.; Jakobs, S.; Warscheid, B.; Rehling, P.: Silencing mitochondrial gene expression in living cells. Science 389 (6759), 477 (2025)

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7.

Journal Article

Karpinska, M. A.; Zhu, Y.; Fakhraei Ghazvini, Z.; Ramasamy, S.; Barbieri, M.; Cao, N. T. B.; Varahram, N.; Aljahani, A.; Lidschreiber, M.; Papantonis, A. et al.; Oudelaar, A. M.: CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation. Nature Structural & Molecular Biology 32, pp. 1268 - 1281 (2025)

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8.

Journal Article

Zhang, L.; Batters, C.; Aibara, S.; Gordiyenko, Y.; Žumer, K.; Schmitzová, J.; Maier, K. C.; Cramer, P.; Zhang, S.: Structure of a transcribing Pol II-DSIF-SPT6-U1 snRNP complex. Nature Communications 16, 5823 (2025)

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9.

Journal Article

Lysakovskaia, K.; Devadas, A.; Schwalb, B.; Lidschreiber, M.; Cramer, P.: Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition. Nature Structural & Molecular Biology 32, pp. 995 - 1005 (2025)

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supplementary-material

10.

Journal Article

Heinrichs, M.; Finke, A. F.; Aibara, S.; Krempler, A.; Boshnakovska, A.; Rehling, P.; Hillen, H. S.; Richter-Dennerlein, R.: Coupling of ribosome biogenesis and translation initiation in human mitochondria. Nature Communications 16, 3641 (2025)

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11.

Journal Article

Kabinger, F.; Doze, V.; Schmitzová, J.; Lidschreiber, M.; Dienemann, C.; Cramer, P.: Structural basis of SARS-CoV-2 polymerase inhibition by nonnucleoside inhibitor HeE1-2Tyr. Proceedings of the National Academy of Sciences of the United States of America 122 (10), e2419854122 (2025)

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12.

Journal Article

Faul, N.; Chen, S.-Y.; Lamberz, C.; Bruckner, M.; Dienemann, C.; Burg, T. P.: Cryo-iCLEM: Cryo correlative light and electron microscopy with immersion objectives. Journal of Structural Biology 217 (1), 108179 (2025)

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13.

Journal Article

Rengachari, S.; Hainthaler, T.; Oberthür, C.; Lidschreiber, M.; Cramer, P.: Mechanism of polyadenylation-independent RNA polymerase II termination. Nature Structural & Molecular Biology 32, pp. 339 - 345 (2025)

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14.

Journal Article

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)

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15.

Journal Article

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)

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16.

Journal Article

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)

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17.

Journal Article

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)

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18.

Journal Article

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)

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19.

Journal Article

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)

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20.

Journal Article

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)

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pre-print

21.

Journal Article

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)

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22.

Journal Article

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)

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23.

Journal Article

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)

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24.

Journal Article

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

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25.

Journal Article

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)

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26.

Journal Article

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)

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27.

Journal Article

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)

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28.

Journal Article

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)

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publisher-version

29.

Journal Article

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)

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30.

Journal Article

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)

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31.

Journal Article

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

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32.

Journal Article

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)

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33.

Journal Article

Sun, Y.; Wiese, M.; Hmadi, R.; Karayol, R.; Seyfferth, J.; Martinez Greene, J.A.; Erdogdu, N.U.; Deboutte, W.; Arrigoni, L.; Holz, H. et al.; Renschler, G.; Hirsch, N.; Foertsch, A.; Basilicata, M.F.; Stehle, T.; Shvedunova, M.; Bella, C.; Pessoa Rodrigues, C.; Schwalb, B.; Cramer, P.; Manke, T.; Akhtar, A.: MSL2 ensures biallelic gene expression in mammals. Nature 624 (7990), pp. 173 - 181 (2023)

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34.

Journal Article

Chen, Y.; Kokic, G.; Dienemann, C.; Dybkov, O.; Urlaub, H.; Cramer, P.: Structure of the transcribing RNA polymerase II–Elongin complex. Nature Structural & Molecular Biology 30, pp. 1925 - 1935 (2023)

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35.

Journal Article

Palau, A.; Segerberg, F.; Lidschreiber, M.; Lidschreiber, K.; Naughton, A.J.; Needhamsen, M.; Jung, L.A.; Jagodic, M.; Cramer, P.; Lehmann, S. et al.; Carlsten, M.; Lennartsson, A.: Perturbed epigenetic transcriptional regulation in AML with IDH mutations causes increased susceptibility to NK cells. Leukemia 37, pp. 1830 - 1841 (2023)

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36.

Journal Article

Garg, G.; Dienemann, C.; Farnung, L.; Schwarz, J.; Linden, A.; Urlaub, H.; Cramer, P.: Structural insights into human co-transcriptional capping. Molecular Cell 83 (14), pp. 2464 - 2477.e5 (2023)

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37.

Journal Article

Rouvière, J. O.; Salerno-Kochan, A.; Lykke-Andersen, S.; Garland, W.; Dou, Y.; Rathore, O.; Molska, E. Š.; Wu, G.; Schmid, M.; Bugai, A. et al.; Jakobsen, L.; Zumer, K.; Cramer, P.; Andersen, J. S.; Conti, E.; Jensen, T. H.: ARS2 instructs early transcription termination-coupled RNA decay by recruiting ZC3H4 to nascent transcripts. Molecular Cell 83 (13), pp. 2240 - 2257 (2023)

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38.

Journal Article

Ramasamy, S.; Aljahani, A.; Karpinska, M. A.; Cao, N. T. B.; Velychko, T.; Cruz, J. N.; Lidschreiber, M.; Oudelaar, A. M.: The Mediator complex regulates enhancer-promoter interactions. Nature Structural and Molecular Biology 30, pp. 991 - 1000 (2023)

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39.

Journal Article

Abril-Garrido, J.; Dienemann, C.; Grabbe, F.; Velychko, T.; Lidschreiber, M.; Wang, H.; Cramer, P.: Structural basis of transcription reduction by a promoter-proximal +1 nucleosome. Molecular Cell 83 (11), pp. 1798 - 1809.e7 (2023)

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40.

Journal Article

Schmitzová, J.; Cretu, C.; Dienemann, C.; Urlaub, H.; Pena, V.: Structural basis of catalytic activation in human splicing. Nature 617, pp. 842 - 850 (2023)

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41.

Journal Article

Rengachari, S.; Schilbach, S.; Cramer, P.: Mediator structure and function in transcription initiation. Biological Chemistry, aop (2023)

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42.

Journal Article

Schilbach, S.; Wang, H.; Dienemann, C.; Cramer, P.: Yeast PIC-mediator structure with RNA polymerase II C-terminal domain. Proceedings of the National Academy of Sciences of the United States of America 120 (15), e2220542120 (2023)

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43.

Journal Article

Dybkov, O.; Preußner, M.; El Ayoubi, L.; Feng, V.-Y.; Harnisch, C.; Merz, K.; Leupold, P.; Yudichev, P.; Agafonov, D. E.; Will, C. L. et al.; Girard, C.; Dienemann, C.; Urlaub, H.; Kastner, B.; Heyd, F.; Lührmann, R.: Regulation of 3′ splice site selection after step 1 of splicing by spliceosomal C* proteins. Science Advances 9 (9), eadf178 (2023)

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44.

Journal Article

Wang, H.; Schilbach, S.; Ninov, M.; Urlaub, H.; Cramer, P.: Structures of transcription preinitiation complex engaged with the +1 nucleosome. Nature Structural and Molecular Biology 30, pp. 226 - 232 (2023)

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45.

Journal Article

Dienemann, C.: Towards automating single-particle cryo-EM data acquisition. IUCRJ 10 (Part 1), pp. 4 - 5 (2023)

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46.

Journal Article

Flores-Solis, D.; Lushpinskaia, I.P.; Polyansky, A.A.; Changiarath, A.; Boehning, M.; Mirkovic, M.; Walshe, J.; Pietrek, L.M.; Cramer, P.; Stelzl, L.S. et al.; Zagrovic, B.; Zweckstetter, M.: Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II. Nature Communications 14 (1), 5979 (2023)

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47.

Journal Article

Rengachari, S.; Schilbach, S.; Kaliyappan, T.; Gouge, J.; Zumer, K.; Schwarz, J.; Urlaub, H.; Dienemann, C.; Vannini, A.; Cramer, P.: Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II. Nature Structural and Molecular Biology 29, pp. 1159 - 1169 (2022)

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48.

Journal Article

Frieg, B.; Antonschmidt, L.; Dienemann, C.; Geraets, J. A.; Najbauer, E. E.; Matthes, D.; de Groot, B. L.; Andreas, L. B.; Becker, S.; Griesinger, C. et al.; Schröder, G. F.: The 3D structure of lipidic fibrils of α-synuclein. Nature Communications 13 (1), 6810 (2022)

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49.

Journal Article

de Opakua, A. I.; Geraets, J. A.; Frieg, B.; Dienemann, C.; Savastano, A.; Rankovic, M.; Cima-Omori, M.-S.; Schröder, G. F.; Zweckstetter, M.: Molecular interactions of FG nucleoporin repeats at high resolution. Nature Chemistry 14, pp. 1278 - 1285 (2022)

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50.

Journal Article

Yahya, G.; Menges, P.; Amponsah, P. S.; Ngandiri, D. A.; Schulz, D.; Wallek, A. U.; Kulak, N. A.; Mann, M.; Cramer, P.; Savage, V. et al.; Raeschle, M.; Storchova, Z.: Sublinear scaling of the cellular proteome with ploidy. Nature Communications 13 (1), 6182 (2022)

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Publications

Journal Article (333)