Disclaimer: This page includes all preprints by NCCR member labs.
Preprints
- M. Pacesa and M. Jinek (2021) Mechanism of R-loop formation and conformational activation of Cas9
bioRxiv - C.E. Dewar, S. Oeljeklaus, J. Mani, W.W.D. Mühlhäuser, B. Warscheid and A. Schneider (2021) Mistargeting of hydrophobic mitochondrial proteins activates a nucleus-mediated posttranscriptional quality control pathway in trypanosomes
bioRxiv - A.B. Eberle, K. Schranz, S. Nasif, L. Grollmus and Oliver Mühlemann (2021) Dissecting the import and export pathways of the human RNA helicase UPF1
bioRxiv - A.J. Hume, B. Heiden, J. Olejnik, E.L. Suder, S. Ross, W.A. Scoon, E. Bullitt, M. Ericsson, M.R. White, J. Turcinovic, T.T.N. Thao, R. M. Hekman, J.E. Kaserman, J. Huang, K. Alysandratos, G.E. Toth, F. Jakab, D.N. Kotton, A.A. Wilson, A. Emili, V. Thiel, J.H. Connor, G. Kemenesi, D. Cifuentes and E. Mühlberger (2021) Recombinant Lloviu virus as a model to study inaccessible zoonotic viruses
bioRxiv - A. Brümmer, R. Dreos, A.C. Marques and S. Bergmann (2021)Analysis of eukaryotic lincRNA sequences reveals signatures of repressed translation in species under strong selection
bioRxiv - M. Hersch, A. Biasini, A.C. Marques and S. Bergmann (2021) Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment
bioRxiv - M. Roganowicz, D. Baer and R. Santoro (2021) BAZ2A-RNA mediated association with TOP2A and KDM1A represses gene expression in prostate cancer
bioRxiv - A. Kroupova, F. Ackle, F.M. Boneberg, A. Chui, S. Weitzer, M. Faini, A. Leitner, R. Aebersold, J. Martinez and M. Jinek (2021) Molecular architecture of the human tRNA ligase complex
bioRxiv - I. Querques, M. Schmitz, S. Oberli, C. Chanez and M. Jinek (2021) Molecular mechanism of target site selection and remodeling by type V CRISPR-associated transposons
bioRxiv - Y.P. Hauser, M.W.M. Meeuse, D. Gaidatzis and H. Grosshans (2021) The BLMP-1 transcription factor promotes oscillatory gene expression to achieve timely molting
bioRxiv - R. Weber, U. Ghoshdastider, D. Spies, C. Dure, F. Valdivia-Francia, M. Forny, M. Ormiston, P.F. Renz, D. Taborsky, M. Yigit, H. Yamahachi and A. Sendoel (2021) Monitoring the 5`UTR landscape reveals 5`terminal oligopyrimidine (TOP) motif switches to drive translational efficiencies
bioRxiv - D. Burri and M. Zavolan (2021) Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism
bioRxiv - L. Ulrich, N.J. Halwe, A. Taddeo, N. Ebert, J. Schön, C. Devisme, B.S. Trüeb, B. Hoffmann, M. Wider, M. Bekliz, M. Essaidi-Laziosi, M.L. Schmidt, D. Niemeyer, V.M. Corman, A. Kraft, A. Godel, L. Laloli, J.N. Kelly, A. Breithaupt, C. Wylezich, I.M. Berenguer Veiga, M. Gultom, K. Adea, B. Meyer, C. Eberhardt, L. Thomann, M. Gsell-Albert, F. Labroussaa, J. Jores, A. Summerfield, C. Drosten, I.A. Eckerle, R. Dijkman, D. Hoffmann, V. Thiel, M. Beer and C. Benarafa (2021) Enhanced fitness of SARS-CoV-2 variant of concern B.1.1.7, but not B.1.351, in animal models
bioRxiv - A. Iyer, M. Niemann, L. Farine, M. Serricchio, A. Schneider and P. Bütikofer (2021) The endoplasmic reticulum membrane protein complex localizes to the mitochondrial - endoplasmic reticulum interface and its subunits modulate phospholipid biosynthesis in Trypanosoma brucei
bioRxiv - P. Dave, E. Griesbach, G. Roth, D. Mateju and J. Chao (2021) Single-molecule imaging reveals the coupling of translation and mRNA decay
bioRxiv - D.J. Ham, A. Boersch, K. Chojnowska, S. Lin, A.B. Leuchtmann, A.S. Ham, M. Thuerkauf, J. Delezie, R. Furrer, D. Burri, M. Sinnreich, C. Handschin, L.A. Tintignac, M. Zavolan, N. Mittal, M.A. Ruegg (2021) Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle
bioRxiv - L.-A. Gurzeler, J. Ziegelmuller, O. Mühlemann and E.D. Karousis (2021) Production of human translation-competent lysates using dual centrifugation
bioRxiv - R. Dijkman, M. Selvaraj, H.H. Gad, S. More, R. Hartmann, S. Perlman, V. Thiel and R. Channappanavar (2021) Effective interferon (IFN)-lambda treatment regimen to control lethal MERS-CoV infection in mice
bioRxiv - K. Tabata, V. Prasad, D. Paul, J.-Y. Lee, M.-T. Pham, W.-I. Twu, C.J. Neufeldt, M. Cortese, B. Cerikan, C.S. Tran, C. Luechtenborg, P. Vkovski, K. Hoermann, A. Mueller, C. Zitzmann, U. Haselmann, J. Beneke, L. Kaderali, H. Erfle, V. Thiel, V. Lohmann, G. Superti-Furga, B. Bruegger and R. Bartenschlager (2021) Convergent use of phosphatidic acid for Hepatitis C virus and SARS-CoV-2 replication organelle formation
bioRxiv - M. Emmenegger, E. De Cecco, M. Hruska-Plochan, T. Eninger, M.M. Schneider, M. Barth, E. Tantardini, P. de Rossi, M. Bacioglu, R.G. Langston, A. Kaganovich, N. Bengoa-Vergniory, A. Gonzalez-Guerra, M. Avar, D. Heinzer, R. Reimann, L.M. Häsler, T.W. Herling, N.S. Matharu, N. Landeck, K. Luk, R. Melki, P.J. Kahle, S. Hornemann, T.P.J. Knowles, M.R. Cookson, M. Polymenidou, M. Jucker and A. Aguzzi (2021) LAG3 is not expressed in human and murine neurons and does not modulate a-synucleinopathies
bioRxiv - E.D. Karousis, F. Gypas, M. Zavolan and O. Mühlemann (2021)Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells
bioRxiv - G. Holzer, P. De Magistris, C. Gramminger, R. Sachdev, A. Magalska, A. Schooley, A. Scheufen, B. Lennartz, M. Tatarek-Nossol, H. Lue, M.I. Linder, U. Kutay, C. Preisinger, D. Moreno-Andres and W. Antonin (2021) The nucleoporin Nup50 activates the Ran guanyl-nucleotide exchange factor RCC1 to promote mitotic NPC assembly
bioRxiv - J.A. Ruland, A.M. Krueger, K.E. Doerner, R. Bhatia, S. Wirths, D. Poetes, U. Kutay, J.P. Siebrasse and U. Kubitscheck (2021) Nuclear export of the pre-60S ribosomal subunit through single nuclear pores observed in real time
bioRxiv - M. Calon, A.A. Malar, S. Pfister, V. Rimal, M.E. Weber, T. Wiegand, J. Zehnder, M. Chavez, R. Deb, R. Cadalbert, A. Dapp, M.-L. Fogeron, A. Hunkeler, L. Lecoq, A. Torosyan, D. Zyla, R. Glockshuber, S. Jonas, M. Nassal, M. Ernst, A. Bockmann and B.H. Meier (2021) Biomolecular solid-state NMR spectroscopy at highest field: the gain in resolution at 1200 MHz
bioRxiv - T. Lenarcic, M. Jaskolowski, M. Leibundgut, A. Scaiola, T. Schoenhut, M. Saurer, R. Lee, O. Rackham, A. Filipovska and N. Ban (2021) Stepwise maturation of the peptidyl transferase region of human mitoribosomes
bioRxiv - B.D. Tobwin and H. Grosshans (2021) A folder mechanism ensures size uniformity among C. elegans individuals by coupling growth and development
bioRxiv - K.M. Hannan, P. Soo, M.S. Wong, J.K. Lee, N. Hein, M. Evers, K.D. Wysoke, T.D. Williams, C. Montellese, L. Smith, S.J. Al-Obaidi, L. Núñez-Villacís, P.a Poh, M. Pavy, J.-S. He, K.M. Parsons, J. Diesch, G. Burgio, R. Ferreira, Z.-P. Feng, C.M. Gould, P.B. Madhamshettiwar, J. Flygare, T.J. Gonda, K.J. Simpson, U. Kutay, R.B. Pearson, C. Engel, N. Watkins, R.D. Hannan and A.J. George (2021) Nuclear stabilisation of p53 requires a functional nucleolar surveillance pathway
bioRxiv - E. Kummer, K.N. Schubert, T. Schönhut, A. Scaiola and N. Ban (2021) Release, rescue and recycling: termination of translation in mammalian mitochondria
bioRxiv - F. Gruhl, P. Janich, H. Kaessmann and D. Gatfield (2021) Circular RNA repertoires are associated with evolutionarily young transposable elements
bioRxiv - A. Kratzel, J.N. Kelly, Y. Brueggemann, J. Portmann, P. V'kovski, D. Todt, N. Ebert, E. Steinmann, R. Dijkman, G. Zimmer, S. Pfaender and V. Thiel (2021) A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets
bioRxiv - M. Krepl, F. Damberger, C. von Schroetter, D. Theler, P. Pokorna, F. Allain and J. Sponer (2021) Recognition of N6-methyladenosine by the YTHDC1 YTH domain studied by molecular dynamics and NMR spectroscopy: The role of hydration
bioRxiv - S. Tetter, N. Terasaka, A. Steinauer, R.J. Bingham, S. Clark, A.P. Scott, N. Patel, M. Leibundgut, E. Wroblewski, N. Ban, P.G. Stockley, R. Twarock and D. Hilvert (2020) Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein
bioRxiv - O. Garcia-Nicolas, P. V'kovski, F. Zettl, G. Zimmer, V. Thiel and A. Summerfield (2020) No evidence for human monocyte-derived macrophage infection and antibody-mediated enhancement of SARS-CoV-2 infection
bioRxiv - B.Th. Eichenberger, Y.X. Zhan, M. Rempfler, L. Girogetti and J. Chao (2020) deepBlink: Threshold-independent detection and localization of diffraction-limited spots
bioRxiv - R.K. Gudipati, K. Braun, F. Gypas, D. Hess, J. Schreier, S.H. Carl, R. Ketting and H. Grosshans (2020) Protease-mediated processing of Argonaute proteins controls small RNA association
bioRxiv - B. Krasniqi, A. Stevaert, B. Van Loy, T. Nguyen, J. Thomas, J. Vandeput, D. Jochmans, V. Thiel, R. Dijkman, W. Dehaen, A. Voet and L. Naesens (2020) Betulonic acid derivatives inhibiting coronavirus replication in cell culture via the nsp15 endoribonuclease
bioRxiv - N. Luithle, J. uit de Bos, R. Hovius, D. Maslennikova, R. Lewis, R. Ungricht, B. Fierz, U. Kutay (2020) Torsin ATPases influence chromatin interaction of the Torsin regulator LAP1
bioRxiv - B. Borsari, A. Abad, C. Coimbra Klein, R. Nurtdinov, A. Esteban, E. Palumbo, M. Ruiz-Romero, M. Sanz, B.R. Correa, R. Johnson, S. Pérez-Lluch, R. Guigó (2020) Dynamics of gene expression and chromatin marking during cell state transition
bioRxiv - M. Gultom, M. Licheri, L. Laloli, M. Wider, M. Straessle, S. Steiner, A. Kratzel, T.T.N. Thao, H. Stalder, J. Portmann, M. Holwerda, P. V'kovski, N. Ebert, N. Stokar-Regenscheit, C. Gurtner, P. Zanolari, H. Posthaus, S. Schuller, A. Moreira-Soto, A. Vicente-Santos, E. Corrales-Aguilar, N. Ruggli, G. Tekes, V. von Messling, B. Sawatsky, V. Thiel, R. Dijkman (2020) Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2
bioRxiv - P. Simmler, C. Cortijo, L.M. Koch, P. Galliker, S. Angori, H.A. Bolck, C. Mueller, A. Vukolic, P. Mirtschink, Y. Christinat, N.R. Davidson, K.-V. Lehmann, G. Pellegrini, C. Pauli, D. Lenggenhager, I. Guccini, T. Ringel, C. Hirt, G. Raetsch, H. Moch, M. Stoffel, G. Schwank (2020) SF3B1 promotes tumor malignancy through splicing-independent co-activation of HIF1alpha
bioRxiv - B. Zhou, T.T.N. Thao, D. Hoffmann, A. Taddeo, N. Ebert, F. Labroussaa, A. Pohlmann, J. King, J. Portmann, N. J. Halwe, L. Ulrich, B.S. Trueb, J.N. Kelly, X. Fan, B. Hoffmann, S. Steiner, L. Wang, L. Thomann, X. Lin, H. Stalder, B. Pozzi, S. de Brot, N. Jiang, D. Cui, J. Hossain, M. Wilson, M.W. Keller, T.J. Stark, J.R. Barnes, R. Dijkman, J. Jores, C. Benarafa, D.E. Wentworth, V. Thiel and M. Beer (2020) SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility
bioRxiv - P.R. Bhatt, A. Scaiola, G. Loughran, M. Leibundgut, A. Kratzel, A. McMillan, K.M. O’ Connor, J.W. Bode, V. Thiel, J.F. Atkins, N. Ban (2020) Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome
bioRxiv - L. Contu, G. Balistreri, M. Domanski, A. Uldry, O. Mühlemann (2020) Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay
bioRxiv - M. Linder, D. Liko, V. Kancherla, S. Piscuoglio, M.N. Hall (2020) Colitis is associated with loss of LHPP and up-regulation of histidine phosphorylation in intestinal epithelial cells
bioRxiv - N. Bakhtina, M. Muller, H. Wischnewski, R. Arora, C. Ciaudo (2020) 3D synthetic microscaffolds promote homogenous expression of NANOG in mouse embryonic stem cells
bioRxiv - L. Plassart, R. Shayan, C. Montellese, D. Rinaldi, N. Larburu, C. Pichereaux, S. Lebaron, M. O’Donohue, U. Kutay, J. Marcoux, P. Gleizes, C. Plisson-Chastang (2020) The final step of 40S ribosomal subunit maturation is controlled by a dual key lock
bioRxiv - A. Vancura, A. Lanzós, N. Bosch, M. Torres, S. Häfliger and R. Johnson (2020) Semi-automated annotation of known and novel cancer long noncoding RNAs with the Cancer LncRNA Census 2 (CLC2)
bioRxiv - N. Bosch, M. Medová, R. Esposito, C. Pulido-Quetglas, Y. Zimmer and R. Johnson (2020) Enhancing CRISPR deletion via pharmacological delay of DNA-PK
bioRxiv - P. Sharma, B.S. Nilges, J. Wu and S.A. Leidel (2019) The translation inhibitor cycloheximide affects ribosome profiling data in a species-specific manner
bioRxiv - S. Reber, H. Lindsay, A. Devoy, D. Jutzi, J. Mechtersheimer, M. Domanski, O. Mühlemann, S.M.L. Barabino and M.-D. Ruepp (2019) The phase separation-dependent FUS interactome reveals nuclear and cytoplasmic function of liquid-liquid phase separation
bioRxiv - S.C. Lenzken, B.R. Levone, G. Filosa, M. Antonaci, F. Conte, C. Kizilirmak, S. Reber, A. Loffreda, F. Biella, A.E. Ronchi, O. Mühlemann, A. Bachi, M.-D. Ruepp and S.M.L. Barabino (2019) FUS-dependent phase separation initiates double-strand break repair
bioRxiv - I. Ferro, J. Gavini, L. Bracher, M. Landolfo, D. Candinas, D. Stroka and N. Polacek (2020) The human vault RNA enhances tumorigenesis and chemoresistance through the lysosome
bioRxiv - G. Yang, C. Heisenberger, I.C. Kos-Braun, N. Polacek, J. Grillari, M. Schosserer and M. Koš1 (2020) Cellular senescence and quiescence are associated with altered ribosomal RNA methylation and processing
bioRxiv - A. Stukalov, V. Girault, V. Grass, V. Bergant, O. Karayel, C. Urban, D.A. Haas, Y. Huang, L. Oubraham, A. Wang, S.M. Hamad, A. Piras, M. Tanzer, F. M. Hansen, T. Enghleitner, M. Reinecke, T.M. Lavacca, R. Ehmann, R. Wölfel, J. Jores, B. Kuster, U. Protzer, R. Rad, J. Ziebuhr, V. Thiel, P. Scaturro, M. Mann and Andreas Pichlmair (2020) Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV
bioRxiv - M. Holwerda, P. V’kovski, M. Wider, V. Thiel and R. Dijkman (2020) Identification of five antiviral compounds from the Pandemic Response Box targeting SARS-CoV-2
bioRxiv - P. V’kovski, M. Gultom, S. Steiner, J. Kelly, J. Russeil, B. Mangeat, E. Cora, J. Pezoldt, M. Holwerda, A. Kratzel, L. Laloli, M. Wider, J. Portmann, T. Tran, N. Ebert, H. Stalder, R. Hartmann, V. Gardeux, D. Alpern, B. Deplancke, V. Thiel and R. Dijkman (2020) Disparate temperature-dependent virus – host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium
bioRxiv - J.N. Kelly, L. Laloli, P. V’kovski, M. Holwerda, J. Portmann, V. Thiel and R. Dijkman (2020) Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis
bioRxiv - N.S. Ravi, B. Wienert, S.K. Wyman, J. Vu, A.A. Pai, P. Balasubramanian, Y. Nakamura, R. Kurita, S. Marepally, S. Thangavel, S.R. Velayudhan, A. Srivastava, M.A. DeWitt, J.E. Corn and K.M. Mohankumar (2020) Identification of novel HPFH-like mutations by CRISPR base editing that elevates the expression of fetal hemoglobin
bioRxiv - R. Baik, S.K. Wyman, S. K. and J.E. Corn (2019) Genome editing to model and reverse a prevalent mutation associated with myeloproliferative neoplasms
bioRxiv - M.M. Duszczyk, H. Wischnewski, T. Kazeeva, F.E. Loughlin, C. von Schroetter, U. Pradère, J. Hall, C. Ciaudo and F.H.-T. Allain (2019) The solution structure of Dead End bound to AU-rich RNA reveals an unprecedented mode of tandem RRM-RNA recognition required for mRNA regulation
bioRxiv - T.C.S. Mak, Y. von Ohlen, Y. Fang Wang, E. Kane, K. Jurgaityte, P. Ervilha, P. Chabosseau, W. Distaso, V. Salem, A. Tomas, M. Stoffel, P. Marchetti, A.M.J. Shapiro, G.A. Rutter and M. Latreille (2019) B-cell dedifferentiation is associated with epithelial-mesenchymal transition triggered by miR-7-mediated repression of mSwi/Snf complex
bioRxiv - J. Scekic-Zahirovic, I. Sanjuan-Ruiz, V. Kan, S. Megat, P. De Rossi, S. Dieterlé, R. Cassel, P. Kessler, D. Wiesner, L. Tzeplaeff, V. Demais, H.-P. Muller, G. Picchiarelli, N. Mishra, S. Dirrig-Grosch, J. Kassubek, V. Rasche, A. Ludolph, A.-L. Boutillier, M. Polymenidou, C. Lagier-Tourenne, S. Liebscher and L. Dupuis (2020) Cytoplasmic accumulation of FUS triggers early behavioral alterations linked to cortical neuronal hyperactivity and defects in inhibitory synapses
bioRxiv - S. Sahadevan, K.M. Hembach, E. Tantardini, M. Pérez-Berlanga, M. Hruska-Plochan, J. Weber, P. Schwarz, L. Dupuis, M.D. Robinson, P. De Rossi and M. Polymenidou (2020) Synaptic accumulation of FUS triggers age-dependent misregulation of inhibitory synapses in ALS-FUS mice
bioRxiv - D. Mateju, B. Eichenberger, J. Eglinger, G. Roth and J.A. Chao (2020) Single-molecule imaging reveals translation of mRNAs localized to stress granules
bioRxiv - A. Scaiola, F. Mangia, S. Imseng, D. Boehringer, K. Berneiser, M. Shimobayashi, E. Stuttfeld, M.N. Hall, N. Ban and T. Maier (2020) The 3.2Å resolution structure of human mTORC2
bioRxiv - M. Shimobayashi, S. Shetty, I.C. Frei, B.K. Wölnerhanssen, D. Weissenberger, N. Dietz, A. Thomas, D. Ritz, A.C. Meyer-Gerspach, T. Maier, N. Hay, R. Peterli, N. Rohner and M.N. Hall (2020) Diet-induced loss of adipose Hexokinase 2 triggers hyperglycemia
bioRxiv - D. Benjamin, M. Colombi, C. Moroni and M.N. Hall (2019) mTOR dependent transformed human cells have a distinct set of essential genes from bcr-abl transformed cells
bioRxiv - S. Ghosh, A. Börsch and M. Zavolan (2020) The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins
bioRxiv - J. Breda, M. Zavolan and E. van Nimwegen (2029) Bayesian inference of the gene expression states of single cells from scRNA-seq data
bioRxiv - C.-Y. Gabriela Lin, A.C. Näger, T. Lunardi, A. Vancevska, G. Lossaint and J. Lingner (2020) The Human Telomeric Proteome During Telomere Replication
bioRxiv - A.-S. Briod, G. Glousker and J. Lingner (2020) RADX Sustains POT1 Function at Telomeres to Counteract RAD51 Binding, which Triggers Telomere Fragility
bioRxiv - J.Y. Tan, B. Abdulkarim and A.C. Marques (2020) Noncanonical targeting contributes significantly to miRNA-mediated regulation
bioRxiv - M. Hersch, A. Biasini, A.C. Marques and S. Bergmann (2020) Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment
bioRxiv - A. Brümmer, R. Dreos, A.C. Marques and S. Bergmann (2020) LincRNA sequences are biased to counteract their translation
bioRxiv - A. Biasini, S. de Pretis, J.Y. Tan, B. Abdulkarim, H. Wischnewski, R. Dreos, M. Pelizzola, C. Ciaudo and A.C. Marques (2020) Translation is required for miRNA-dependent decay of endogenous transcripts
bioRxiv - D. Dalcher, J.Y., C. Bersaglieri, R. Peña-Hernández, E. Vollenweider, S. Zeyen, Ma.W. Schmid, V. Bianchi, S. Butz, R. Kuzyakiv, T. Baubec, A.C. Marques and R. Santoro (2019) TIP5 safeguards genome architecture of ground-state pluripotent stem cells
bioRxiv - R. Peña-Hernández, R. Aprigliano, S. Frommel, K. Pietrzak, S. Steiger, M. Roganowicz, J. Bizzarro and R. Santoro (2020) BAZ2A association with H3K14ac is required for the dedifferentiation of prostate cancer cells into a cancer stem-like state
bioRxiv