Dr. Marc-David Ruepp

Departement für Chemie und Biochemie

E-Mail
marc.ruepp@dcb.unibe.ch
Büro
S175
Postadresse
Freiestrasse 3
CH - 3012 Bern
Sprechstunde
nach Vereinbarung
Präsenzzeiten
Montag bis Freitag

Links

  • 2001-2005: Studies in Biochemistry at the University of Bern, Switzerland: Diploma thesis on pre-mRNA 3’ end processing in the lab of Daniel Schümperli, Institute of Cell Biology.
  • 2006-2009: Ph.D. in the lab of Daniel Schümperli, Institute of Cell Biology, University of Bern. Work on mRNA 3’ end formation and gene expression.
  • 2010-2013: Postdoctoral work in the lab of Oliver Mühlemann, Dept. of Chemisty and Biochemistry, University of Bern. Work on the roles of FUS in RNA metabolism and ALS pathogenesis and on post-transcriptional gene regulation.
  • 2013-2014: Project leader in the group of Prof. Oliver Mühlemann, Dept. of Chemisty and Biochemistry, University of Bern.
  • 2015-present: Junior group leader at the Department of Chemistry and Biochemistry, University of Bern.

My group investigates gene regulation in human cells. Our goal is to decipher the roles of Fused in Sarcoma (FUS) in RNA metabolism and the roles of FUS mutations in the pathogenesis of the terminal neurodegenerative disease Amyotrophic Lateral Sclerosis (ALS). Furthermore, in collaboration with Martin Lochner (University of Bern) and Andrew J. Thompson (University of Cambridge) we try to understand the molecular pharmacology of several neuronal receptors.

Journal Article

Jack, Thomas; Leuenberger, Michele; Ruepp, Marc-David; Vernekar, Sanjeev Kumar V; Thompson, Andrew James; Braga-Lagache, Sophie; Heller, Manfred; Lochner, Martin (2019). Mapping the Orthosteric Binding Site of the Human 5-HT3 Receptor Using Photo-crosslinking Antagonists. ACS chemical neuroscience, 10(1), pp. 438-450. American Chemical Society 10.1021/acschemneuro.8b00327

Loughlin, Fionna E.; Lukavsky, Peter J.; Kazeeva, Tamara; Reber, Stefan; Hock, Eva-Maria; Colombo, Martino; Von Schroetter, Christine; Pauli, Phillip; Cléry, Antoine; Mühlemann, Oliver; Polymenidou, Magdalini; Ruepp, Marc-David; Allain, Frédéric H.-T. (2019). The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity. Molecular cell, 73(3), 490-504.e6. Cell Press 10.1016/j.molcel.2018.11.012

Reber, Stefan; Mechtersheimer, Jonas Matthias; Nasif, Sofia; Benitez, Julio Aguila; Colombo, Martino; Domanski, Michal; Jutzi, Daniel; Hedlund, Eva; Ruepp, Marc-David; Matera, A. Gregory (2018). CRISPR-Trap: a clean approach for the generation of gene knockouts and gene replacements in human cells. Molecular biology of the cell, 29(2), pp. 75-83. American Society for Cell Biology 10.1091/mbc.E17-05-0288

Ruepp, Marc-David; Wei, Hao; Leuenberger, Michele; Lochner, Martin; Thompson, Andrew James (2017). The binding orientation of structurally-related ligands can differ; A cautionary note. Neuropharmacology, 119, pp. 48-61. Elsevier 10.1016/j.neuropharm.2017.01.023

Thompson, Andrew J.; Metzger, Simon; Lochner, Martin; Ruepp, Marc-David (2017). The binding orientation of epibatidine at α7 nACh receptors. Neuropharmacology, 116, pp. 421-428. Elsevier 10.1016/j.neuropharm.2017.01.008

Reber, Stefan; Stettler, Jolanda; Filosa, G.; Colombo, Martino; Jutzi, D.; Lenzken, S. C.; Schweingruber, Christoph; Bruggmann, Rémy; Bachi, A.; Barabino, S. M.; Mühlemann, Oliver; Ruepp, Marc-David (2016). Minor intron splicing is regulated by FUS and affected by ALS-associated FUS mutants. EMBO journal, 35(11) Nature Publishing Group 10.15252/embj.201593791

Suárez-Calvet, Marc; Neumann, Manuela; Arzberger, Thomas; Abou-Ajram, Claudia; Funk, Eva; Hartmann, Hannelore; Edbauer, Dieter; Kremmer, Elisabeth; Göbl, Christoph; Resch, Moritz; Bourgeois, Benjamin; Madl, Tobias; Reber, Stefan; Jutzi, Daniel; Ruepp, Marc-David; Mackenzie, Ian R. A.; Ansorge, Olaf; Dormann, Dorothee; Haass, Christian (2016). Monomethylated and unmethylated FUS exhibit increased binding to Transportin and distinguish FTLD-FUS from ALS-FUS. Acta neuropathologica, 131(4), pp. 587-604. Springer 10.1007/s00401-016-1544-2

Schweingruber, Christoph; Soffientini, Paolo; Ruepp, Marc-David; Bachi, Angela; Mühlemann, Oliver (2016). Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID). PLoS ONE, 11(3), e0150239. Public Library of Science 10.1371/journal.pone.0150239

Barden, Adam O.; Goler, Adam S.; Humphreys, Sara C.; Tabatabaei, Samaneh; Lochner, Martin; Ruepp, Marc-David; Jack, Thomas; Simonin, Jonathan; Thompson, Andrew James; Jones, Jeffrey P.; Brozik, James A. (2015). Tracking individual membrane proteins and their biochemistry: The power of direct observation. Neuropharmacology, 98, pp. 22-30. Elsevier 10.1016/j.neuropharm.2015.05.003

Jack, Thomas; Simonin, Jonathan; Ruepp, Marc-David; Thompson, Andrew James; Gertsch, Jürg; Lochner, Martin (2015). Characterizing New Fluorescent Tools for Studying 5-HT3 Receptor Pharmacology. Neuropharmacology, 90, pp. 63-73. Elsevier 10.1016/j.neuropharm.2014.11.007

Raczynska, Katarzyna Dorota; Ruepp, Marc-David; Brzek, Aleksandra; Reber, Stefan; Romeo, Valentina; Rindlisbacher, Barbara; Heller, Manfred; Szweykowska-Kulinska, Zofia; Jarmolowski, Artur; Schümperli, Daniel (2015). FUS/TLS contributes to replication-dependent histone gene expression by interaction with U7 snRNPs and histone-specific transcription factors. Nucleic acids research, 43(20), pp. 9711-9728. Oxford University Press 10.1093/nar/gkv794

Ruepp, Marc-David; Brozik, James A.; de Esch, Iwan J.P.; Farndale, Richard W.; Murrell-Lagnado, Ruth D.; Thompson, Andrew J. (2015). A fluorescent approach for identifying P2X1 ligands. Neuropharmacology, 98, pp. 13-21. Elsevier 10.1016/j.neuropharm.2015.05.016

Jack, Thomas; Ruepp, Marc-David; Thompson, Andrew J.; Mühlemann, Oliver; Lochner, Martin (2014). Synthesis and Characterization of Photoaffinity Probes that Target the 5-HT<SUB>3</SUB> Receptor. CHIMIA, 68(4), pp. 239-242. Bern: Schweizerische Chemische Gesellschaft 10.2533/chimia.2014.239

Nizzardo, Monica; Simone, Chiara; Salani, Sabrina; Ruepp, Marc-David; Rizzo, Federica; Ruggieri, Margherita; Zanetta, Chiara; Brajkovic, Simona; Moulton, Hong M.; Mühlemann, Oliver; Bresolin, Nereo; Comi, Giacomo P.; Corti, Stefania (2014). Effect of Combined Systemic and Local Morpholino Treatment on the Spinal Muscular Atrophy Δ7 Mouse Model Phenotype. Clinical therapeutics, 36(3), 340-356.e5. Elsevier 10.1016/j.clinthera.2014.02.004

Metze, Stefanie; Herzog, Veronika A.; Ruepp, Marc-David; Mühlemann, Oliver (2013). Comparison of EJC-enhanced and EJC-independent NMD in human cells reveals two partially redundant degradation pathways. RNA - a publication of the RNA Society, 19(10), pp. 1432-1448. Woodbury, N.Y.: Cold Spring Harbor Laboratory Press 10.1261/rna.038893.113

Vivarelli, Silvia; Lenzken, Silvia C.; Ruepp, Marc-David; Ranzini, Francesco; Maffioletti, Andrea; Alvarez, Reinaldo; Mühlemann, Oliver; Barabino, Silvia M. L.; Buratti, Emanuele (2013). Paraquat Modulates Alternative Pre-mRNA Splicing by Modifying the Intracellular Distribution of SRPK2. PLoS ONE, 8(4), e61980. Lawrence, Kans.: Public Library of Science 10.1371/journal.pone.0061980

Ruepp, Marc-David; Schweingruber, Christoph; Kleinschmidt, Nicole; Schümperli, Daniel (2011). Interactions of CstF-64, CstF-77, and symplekin: Implications on localisation and function. Molecular biology of the cell, 22(1), pp. 91-104. Bethesda, Md.: American Society for Cell Biology 10.1091/mbc.E10-06-0543

Ruepp, Marc-David; Schümperli, Daniel; Barabino, Silvia M.L. (2011). mRNA 3' end processing and more - multiple functions of mammalian cleavage factor I-68. RNA - a publication of the RNA Society, 2(1), pp. 79-91. Woodbury, N.Y.: Cold Spring Harbor Laboratory Press 10.1002/wrna.35

Ruepp, Marc-David; Vivarelli, Silvia; Pillai, Ramesh S.; Kleinschmidt, Nicole; Azzouz, Teldja N.; Barabino, Silvia M.L.; Schümperli, Daniel (2010). The 68 kDa subunit of mammalian cleavage factor I interacts with the U7 small nuclear ribonucleoprotein and participates in 30-end processing of animal histone mRNAs. Nucleic acids research, 38(21), pp. 7637-7650. London: Oxford University Press 10.1093/nar/gkq613

Meyer, Kathrin; Marquis, Julien; Trüb, Judith; Nlend Nlend, Rachel; Verp, Sonia; Ruepp, Marc-David; Imboden, Hans; Barde, Isabelle; Trono, Didier; Schümperli, Daniel (2009). Rescue of a severe mouse model for spinal muscular atrophy by U7 snRNA-mediated splicing modulation. Human molecular genetics, 18(3), pp. 546-555. Oxford: Oxford University Press 10.1093/hmg/ddn382

Ruepp, Marc-David; Aringhieri, Chiara; Vivarelli, Silvia; Cardinale, Stefano; Paro, Simona; Schümperli, Daniel; Barabino, Silvia M.L. (2009). Mammalian pre-mRNA 3' end processing factor CF I m 68 functions in mRNA export. Molecular biology of the cell, 20(24), pp. 5211-23. Bethesda, Md.: American Society for Cell Biology 10.1091/mbc.E09-05-0389

Conference or Workshop Item

Lochner, Martin; Jack, Thomas; Simonin, Jonathan; Leuenberger, Michele; Rüefli, Pascal; Bur-Cecilio Hechavarria, Yamileidi; Ruepp, Marc-David; Thompson, Andrew J. (August 2016). Investigation of the interaction between 5-HT3R and its modulators: progress in understanding the agonist binding site. CHIMIA, 70(7/8), MC121. Schweizerische Chemische Gesellschaft

Leuenberger, Michele; Ritler, Andreas; Aerni, Valerie; Metzger, Simon G.; Ruepp, Marc-David; Lochner, Martin (August 2016). New insights into glutamate transport in brain: Concise asymmetric synthesis of TFB-TBOA and photoaffinity probes. CHIMIA, 70(7/8), MC123. Schweizerische Chemische Gesellschaft

Leuenberger, Michele; Jack, Thomas; Ruepp, Marc-David; Lagache, Sophie; Heller, Manfred; Mühlemann, Oliver; Thompson, Andrew J.; Lochner, Martin (15 June 2015). Synthesis of photo-crosslinking probes and their application for the site-selective chemical modification of the 5-HT3 receptor (Unpublished). In: Challenges in Chemical Biology (ISACS16). Book of Abstracts. ETH Zürich, Hönggerberg, Switzerland. 15.06.-18.06.2015.

Ruepp, Marc-David (22 October 2014). The FUS(s) about splicing (Unpublished). In: TERM meeting 2014. Paris, Frankreich. 22.10.-23.10.2014.

Lochner, Martin; Jack, Thomas; Simonin, Jonathan; Ruepp, Marc-David; Leuenberger, Michele; Hemmings, Jennifer Luise; Singhanat, Suradech; Thompson, Andrew James (2 October 2014). Studying Ion Channels and Receptors Using Synthetic Molecular Probes (Unpublished). In: 3rd Swiss-Japanese Chemical Biology Symposium. Bern, Switzerland. 02.-03.10.2014.

Lochner, Martin; Jack, Thomas; Simonin, Jonathan; Singhanat, Suradech; Leuenberger, Michele; Ruepp, Marc-David; Hemmings, Jennifer Luise; Thompson, Andrew James (20 August 2014). Synthesis of Molecular Tools for the Cellular Study of Ion Channels and Receptors (Unpublished). In: EMBO Conference Chemical Biology. Heidelberg, Germany. 20.-23.08.2014.

Ruepp, Marc-David (24 January 2014). The role of FUS in splicing regulation (Unpublished). In: Swiss RNA Workshop 2014. Bern, Schweiz. 24.01.2014.

Ruepp, Marc-David (24 January 2014). Genetic Engineering of Induced Pluripotent Stem Cells and Reprogramming to Motor Neurons to Elucidate Selective Motor Neuron Death in Amyotrophic Lateral Sclerosis (Unpublished). In: Swiss RNA Workshop 2014. Bern, Schweiz. 24.01.2014.

Ruepp, Marc-David (24 January 2014). Characterization of the role of the RNA-binding protein FUS in the DNA damage response (Unpublished). In: Swiss RNA Workshop 2014. Bern, Schweiz. 24.01.2014.

Ruepp, Marc-David (24 January 2014). Proteomic characterization of the FUS/TLS interactome (Unpublished). In: Swiss RNA Workshop 2014. Bern, Schweiz. 24.01.2014.

Ruepp, Marc-David (6 September 2013). Synthesis and testing of photoaffinity probes for the site-selectivechemical modifications of the 5-HT3 receptor (Unpublished). In: 2013 Fall Meeting EPFL Lausanne. EPFL Lausanne, CH. 06.09.2013.

Ruepp, Marc-David (12 August 2013). Synthesis and testing of photoaffinity probes for the site-selective chemical modifications of the 5-HT3 receptor (Unpublished). In: Swiss Summer School 2013 in Synthesis and Catalysis. Villars, CH. 12.-16.08.2013.

Jack, Thomas; Ruepp, Marc-David; Mühlemann, Oliver; Thompson, Andrew James; Lummis, Sarah C. R.; Lochner, Martin (August 2013). Synthesis and testing of photoaffinity probes for the site-selective chemical modification of the 5-HT3 receptor. CHIMIA, 67(7/8), p. 519. Schweizerische Chemische Gesellschaft

Simonin, Jonathan; Jack, Thomas; Ruepp, Marc-David; Hothersall, Daniel; Connolly, Christopher; Chicca, Andrea; Gertsch, Jürg; Thompson, Andrew James; Lummis, Sarah C. R.; Lochner, Martin (August 2013). Synthesis of fluorescent probes for the study of the 5-HT3 receptor: applications in imaging and fluorescence polarization. CHIMIA, 67(7/8), p. 524. Schweizerische Chemische Gesellschaft

Singhanat, Suradech; Ruepp, Marc-David; Jack, Thomas; Rougier, Jean-Sébastien; Abriel, Hugues; Mühlemann, Oliver; Lochner, Martin (August 2013). Towards the site-specific modification of the hERG K+ channel. CHIMIA, 67(7/8), p. 532. Schweizerische Chemische Gesellschaft

Ruepp, Marc-David (11 June 2013). The FUS protein is required for cell proliferation (Unpublished). In: 18th International Annual Meeting of the RNA Society. Davos, CH. 11.-15.06.2013.

Ruepp, Marc-David (11 June 2013). Combined systemic and local morpholino treatment rescues the phenotype of the SMA Delta 7 mouse model (Unpublished). In: 18th International Annual Meeting of the RNA Society. Davos, CH. 11.-15.06.2013.

Ruepp, Marc-David (11 June 2013). Characterization of the potential role for RNA-binding protein FUS in DNA damage response: A quantitative proteomic approach (Unpublished). In: 18th International Annual Meeting of the RNA Society. Davos, CH. 11.-15.06.2013.

Ruepp, Marc-David (11 June 2013). The involvement of miRNA Dysregulation in Amyotrophic Lateral Sclerosis (Unpublished). In: 18th International Annual Meeting of the RNA Society. Davos, CH. 11.-15.06.2013.

Ruepp, Marc-David (11 June 2013). FUS protein interacts with U7 snRNP and plays a role in replication-dependant histone genes expression (Unpublished). In: 18th International Annual Meeting of the RNA Society. 11.-15.06.2013.

Ruepp, Marc-David (10 June 2013). Synthesis and testing of photoaffinity probes for the site-selectivechemical modifications of the 5-HT3 receptor (Unpublished). In: CUSO Subject Day "Modern Synthetic Methods and their Application in the Context of Natural Products". Neuchâtel, CH. 10.-11.06.2013.

Lochner, Martin; Jack, Thomas; Simonin, Jonathan; Singhanat, Suradech; Hemmings, Jennifer Luise; Leuenberger, Michele; Ruepp, Marc-David; Thompson, Andrew James (9 June 2013). Synthesis of Molecular Tools for the Cellular Study of Ion Channels and Receptors (Unpublished). In: Gordon Research Conference Bioorganic Chemistry. Andover, NH, USA. 09.-14.06.2013.

Lochner, Martin; Jack, Thomas; Simonin, Jonathan; Singhanat, Suradech; Hemmings, Jennifer Luise; Leuenberger, Michele; Thompson, Andrew James; Ruepp, Marc-David (26 April 2013). Chemical Tools for the Study and Modification of Ion Channels and Receptors (Unpublished). In: BioChemLig Meeting. Bern. 26.04.2013.

Ruepp, Marc-David (25 January 2013). Characterization of the potential role for RNA-binding protein FUS/TLS in DNA damage response: A quantitative proteomic approach (Unpublished). In: Swiss RNA Workshop 2013. Bern, CH. 25.01.2013.

Ruepp, Marc-David (25 January 2013). The multifunctional FUS protein: Characterization of the biological effects of its depletion (Unpublished). In: Swiss RNA Workshop 2013. Bern, CH. 25.01.2013.

Ruepp, Marc-David (25 January 2013). Unravelling the multiple roles of FUS in RNA processing and on ALS pathogenesis (Unpublished). In: Swiss RNA Workshop 2013. Bern, CH. 25.01.2013.

Ruepp, Marc-David (25 January 2013). Unravelling the impact of microRNA on Amyotrophic Lateral Sclerosis (ALS) pathogenesis (Unpublished). In: Swiss RNA Workshop 2013. Bern, CH. 25.01.2013.

Ruepp, Marc-David (11 January 2013). Synthesis and testing of photoaffinity probes for the site-selective chemical modifications of the 5-HT3 receptor (Unpublished). In: 11th Swiss Snow Symposium 2013. Saas-Fee, CH. 11.-13.01.2013.

Ruepp, Marc-David; Schweingruber, Christoph; Kleinschmidt, Nicole; Schümperli, Daniel (2010). Interactions of symplekin, CstF-64, and CstF-77. Implications for localisation, stability and function. In: The Fifteenth Annual Meeting of the RNA Society Seattle, Washington USA, June 22-26, 2010 (p. 1). RNA Society

  • ALS Schweiz
  • RNA society
  • Swiss Society for Molecular and Cellular Biosciences (SSMCB), a part of Life Science Switzerland (LS2)