The roles of Trim15 and UCHL3 in the ubiquitin-mediated cell cycle regulation Katerina Jerabkova To cite this version: Katerina Jerabkova. The roles of Trim15 and UCHL3 in the ubiquitin-mediated cell cycle regulation. Cellular Biology. Université de Strasbourg; Univerzita Karlova (Prague), 2019. English. NNT : 2019STRAJ034. tel-02884583 HAL Id: tel-02884583 https://tel.archives-ouvertes.fr/tel-02884583 Submitted on 30 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ DE STRASBOURG ÉCOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ IGBMC - CNRS UMR 7104 - Inserm U 1258 THÈSE présentée par : Kateřina JEŘÁBKOVÁ soutenue le : 09 Octobre 2019 pour obtenir le grade de : Docteur de l’université de Strasbourg Discipline/ Spécialité : Aspects moléculaires et cellulaires de la biologie Les rôles de Trim15 et UCHL3 dans la régulation, médiée par l’ubiquitine, du cycle cellulaire. The roles of Trim15 and UCHL3 in the ubiquitin-mediated cell cycle regulation. THÈSE dirigée par : Mme SUMARA Izabela PhD, Université de Strasbourg Mme CHAWENGSAKSOPHAK Kallayanee PhD, Charles University RAPPORTEURS : Mr LEON Sébastien PhD, Institut Jacques Monod Mr THORPE Peter PhD, Queen Mary University of London AUTRES MEMBRES DU JURY : Mr MENDOZA Manuel PhD, Université de Strasbourg Mr ŠOLC Petr PhD, Charles University Mr SEDLÁČEK Radislav PhD, Charles University -1- CO-TUTELLE PhD THESIS between Charles University (Czech Republic) Faculty of Science - Developmental and Cell Biology and University of Strasbourg (France) École doctorale des sciences de la vie et de la santé - ED 414 The roles of Trim15 and UCHL3 in the ubiquitin-mediated cell cycle regulation. Author: Kateřina Jeřábková Co-supervised by: Izabela Sumara, PhD Kallayanee Chawengsaksophak, PhD Assoc. Prof. Radislav Sedláček, PhD Committee members: Assoc. Prof. Petr Šolc, PhD Peter Thorpe, PhD Manuel Mendoza, PhD Sebastien Leon, PhD Strasbourg 2019 -2- DECLARATION I declare that I wrote the thesis myself and that I cited all the information sources and literature. This work or a substantial part of it was not presented to obtain another academic degree or equivalent. Prague .......................... ........................................... Kateřina Jeřábková FINANCIAL SUPPORT Charles University in Prague (doctoral fellowship), Fellowship from the French Government awarded by the Ministry for foreign affairs to study PhD in a co-tutelle program, Ligue Nationale Contre le Cancer (fellowship for the 4th year), LabEx. -3- Acknowledgements Words cannot explain how grateful I am for all the help I have received from everybody around me during my PhD, it has been a long journey and it seems almost unbelievable that I am writing this text, because it means that I have finished writing my thesis. During my PhD I have entered two labs in two different countries and I found many great people and good friends at both places. First of all, I would like to thank my three supervisors: Iza, Radek and Kallayanee who agreed to take me as a co-tutelle student which was a very challenging arrangement, but also a great experience. I would also like to thank Peter Thorpe, Sebastien Leon, Petr Šolc and Manuel Mendoza for agreeing to evaluate my thesis and to be part of my thesis committee. Special thanks belong to Iza for supervising my work on the UCHL3 project which was a big part of my PhD. I am very thankful that I got the opportunity to work in her lab and to contribute to this very exciting project in a nice lab atmosphere. I would especially like to thank Iza for the trust she gave me in choosing the scientific questions and the experimental setup. This complete support of my work was incredibly valuable and taught me a lot how to eventually become an independent scientist. I hope I will put this to good use in my future career. I would also like to thank Radek for taking me as a PhD student to join his lab and for supporting my idea to start a co tutelle study program. It was definitely not an easy way to go, but I am very grateful for this experience. My big thanks also belong to Kallayanee who was my supervisor at the Charles University and who was always giving me useful advice and supporting me throughout my whole study. I am also very grateful to Trevor for his comments to my project and also for correcting my application to the PhD program. I would like to thank all the members of Iza’s lab (Charlotte, Sushil, Arantxa, Eva, Yongrong and Paulo as well as the former members Steff and Ksenia) for their everyday help and support and especially to Yongrong who participated on the project and helped me with some key experiments. I would also like to thank Charlotte who helped me with cloning and who always made sure nothing is missing in the lab, which made the work much easier. Big thanks belong to Arantxa for great discussions about our projects, for the endless splitting of my cells and for being there for me whenever I needed help. I would like to thank Romeo Ricci and his team for the fruitful discussions during our lab meetings, it taught me how to develop critical thinking which I value a lot. -4- I also thank Snezhka Oliferenko, Didier Devys and Manuel Mendoza who were part of my mid-thesis committee and gave me very valuable comments on my project. I would like to thank Bill Keyes for discussing my project and also to Daniel from Bill’s lab for teaching me how to use the Cell Profiler. I would like to thank all the platforms at IGBMC and at IMG for facilitating my work, especially the cell culture facility, mediaprep, microscopy facility, flow cytometry and the glass washing service. Special and very big thanks belong to Matej who supported me in all aspects of the PhD and who helped me not only experimentally, but who also endlessly discussed my project and pointed out many important aspects of it. I would also like to thank Dominika, Silvia, Jolana, Petr, Olga and Lenka from Radek’s lab for teaching me different methods in the beginning of my PhD, because everything was very new and complicated. Special thanks belong to Björn Schuster who taught me many techniques regarding genome editing. I also thank Veronika, Shohag and Katka, my PhD labmates in Prague. Special thanks belong to Christiana who was always telling me that I can do it [the PhD] and for teaching me how to kill mice (ironically, always before lunch). I would also like to thank Martin for helping me with the migration experiments and to David for the large scale migration and proliferation assays. Many thanks belong to Marina with whom I collaborated on one project and who gave me many valuable scientific advices. I would like to thank all of my friends in Prague and in Strasbourg for being there for me at all times. Especially to Xieyang who helped me to practice all my big presentations (Xieyang, I hope you will Skype me before the thesis defense). I also thank to all my climbing friends whom I have abandoned around the fourth year of my PhD, but they never lost hope that I would come back climbing including Sandrine, Alastair, Arantxa, Xieyang, Renee, Yasmine, Merce, Irene, Vincent, Rocio and many more. Special thanks belong also to people who shared daily lunches and coffees with me and discussed science fun facts with me (Arantxa, Paulo, Alexia, Jordi, Xenia, Matej, Charlotte, Saurabh, Greg, Robert, Bea, Marina, Dimitra and Paula). I would like to also thank my closest friends, to my partner and to my family for the great amount of help, support and patience. Mami, tati, Helčo, Lucie, Mateji, díky moc za všechno, bylo to náročné, ale povedlo se, bez vás by to nešlo! -5- Contents CO-TUTELLE PHD THESIS ............................................................................................................. 2 DECLARATION ............................................................................................................................. 3 FINANCIAL SUPPORT ................................................................................................................... 3 ACKNOWLEDGEMENTS ............................................................................................................... 4 ABSTRACT (ENGLISH) ................................................................................................................ 10 ABSTRAKT (CZECH) .................................................................................................................... 12 SUMMARY (FRENCH) ................................................................................................................ 14 PROJECTS OUTLOOK ................................................................................................................. 20 LIST OF ABBREVIATIONS ............................................................................................................ 22 1 INTRODUCTION ............................................................................................................. 26 1.1 Ubiquitination .................................................................................................................................