Structural and functional studies on epigenetic regulators Jan Kadlec To cite this version: Jan Kadlec. Structural and functional studies on epigenetic regulators. Biomolecules [q-bio.BM]. Université Grenoble Alpes, 2017. tel-02440134 HAL Id: tel-02440134 https://hal.univ-grenoble-alpes.fr/tel-02440134 Submitted on 15 Jan 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. Structural and functional studies on epigenetic regulators Habilitation à diriger des recherches Spécialité: Biologie Jan KADLEC UNIVERSITE GRENOBLE ALPES 2017 ! Date de soutenance : 9 Mars 2017 ECOLE DOCTORALE DE CHIMIE ET SCIENCES DU VIVANT UNIVERSITE GRENOBLE ALPES HABILITATION A DIRIGER DES RECHERCHES Jan KADLEC Title: Structural and functional studies on epigenetic regulators Jury: Prof. Marc Jamin Rapporteur! Dr. Christophe Romier ! Rapporteur Dr. Sbastien Fribourg! Rapporteur Prof. Thomas Schalch ! Examinateur Dr. André Verdel ! Examinateur Institut de Biologie Structurale, Grenoble! Summary This manuscript describes my research activities over the last fifteen years. I graduated in Molecular Biology from the Charles University in Prague in 2000. At that time, structural biology was very poorly developed in my home country. During my training at EMBL in Grenoble I discovered for the first time the world of protein structures and realized how important detailed structural information can be to understand protein function. I then joined the laboratory of Stephen Cusack at the EMBL and began my PhD jointly with the Université Joseph Fourier. I started using X-ray crystallography and studied proteins involved in targeted mRNA degradation pathway called the Nonsense Mediated mRNA Decay. For my postdoc I decided to change the research filed and joined the group of David Stuart at the University of Oxford to work on viral fusion proteins. The preparation of these viral surface glycoproteins for crystallization required their expression in mammalian cells and an efficient deglycosylation. The scientific, instrumentation and technological environment at the department was truly exceptional so it was possible to succeed in these projects in a relatively short time. The structure of the baculovirus fusion protein GP64 we determined was perhaps the most revealing structure I have worked on so far and was a significant contribution to the viral fusion field. While working in Oxford was a great experience I decided to return to France and was offered a staff scientist position back at EMBL Grenoble in my original PhD laboratory. I was very fortunate to be given a maximal scientific independence and support within the group. I established a new research line in the group focusing on epigenetic regulatory complexes. Chromatin/epigenetic control of DNA-based processes is an extremely important and sophisticated layer of regulation. Perhaps, due to the challenging nature of chromatin regulatory complexes for structural analysis, most of them still remain structurally uncharacterised. I started two very fruitful collaborations with expert cell biologist in the chromatin field, Asifa Akhtar (MPI Freiburg) and Bernard de Massy (IGH Montpellier). Together with them we can carry out an interdisciplinary research combining biochemistry, structural and cell biology and genetics. All my work on the histone acetyltransferase complexes (MSL and NSL complex) and PRDM9 at the EMBL included supervision of Master and PhD students. In 2014, I obtained the ATIP/AVENIR start-up grant and moved to the Institut de Biologie Structurale (IBS) in Grenoble where I set up my research team. We continue our effort to structurally and functionally characterise the MSL and NSL complexes as well as the PRDM9 methyltransferase. Given the large size of these complexes, the method of choice for the analysis will be a combination of X-ray crystallography and cryo-electron microscopy. ! Table of contents I. Curriculum vitae ..….…………………………………………………………….……………………….....4 II. List of publications ...…..…………………………………………..…………………….…………….....7 III. Scientific supervision ..………………………………………………………………………………….9 IV. Previous research activities Thesis work at EMBL Grenoble (2000-2005) ………………………………………………......................10 Postdoctoral work at the University of Oxford (2005-2007) ………………….……………………………28 V. Current Research EMBL Grenoble (2008-2015) and IBS Grenoble (since 2015) ………………………..………………….38 - PRDM histone methyltransferases ………………………..……………………………………………….39 - Mof acetyltransferase containing complexes ………………………….……………………………….....50 MSL complex ..……..…………………………………………………..……………………………………...50 NSL complex ………..………………………………………………..………………………………………..76 ! 3 I. Curriculum Vitae • PERSONAL INFORMATION Name: KADLEC Jan http://orcid.org/0000-0002-4853-6918 Date of birth: 12.05.1976 Nationality: Czech Married, 2 children Address: Institut de Biologie Structurale (IBS), 71 avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France Tel: 0457428776 E-Mail: [email protected] Website: http://www.ibs.fr/research/research-groups/ebev/epigenetic-regulators • EDUCATION 2001 - 2005 PhD in Structural Biology Joint PhD degree at the European Molecular Biology Laboratory (EMBL) and Université Joseph Fourier in Grenoble, France. 1998 - 2000 Master degree in Molecular Biology, Faculty of Science, Charles University in Prague, Czech Republic. 1995 - 1998 Bachelor degree in Biology, Faculty of Science, Charles University in Prague, Czech Republic. • CURRENT POSITION Since 2015 Team leader - Institut de Biologie Structurale (IBS), Grenoble, France Epigenetic Regulators team Since 2016 Permanent CR1 researcher – INSERM • PROFFESIONAL EXPERIENCE 2009 - 2015 Staff Scientist at EMBL - Grenoble Outstation (with Stephen Cusack) Structural analysis of epigenetic regulators. 2008 Postdoctoral fellow at EMBL - Grenoble Outstation, France (with Stephen Cusack). 2005 - 2007 Postdoctoral fellow - The Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, UK. Structural analysis of viral fusion proteins (with David Stuart). 2001 - 2005 PhD thesis at EMBL - Grenoble Outstation, France. Structural analysis of Nonsense- Mediated mRNA Decay regulators (with Stephen Cusack). 2000 - 2001 Training at EMBL - Grenoble Outstation, France. Structural analysis of the SNARE complex. (with Winfried Weissenhorn). 1998 - 2000 Undergraduate training in the Laboratory of Physiology and Genetics of Actinomycetes at Institute of Microbiology in Prague. Biosynthetic pathways of lincosamid antibiotics (with Jiri Janata) ! 4 • GRANTS AND FELLOWSHIPS 2016 - Labex Gral - Individual projects (120k EUR) 2015 - Fondation ARC - Projet Fondation ARC (50k EUR) 2014 - ATIP/AVENIR start-up grant - CNRS/Plan Cancer (360k EUR+ salary) 2006 - Marie Curie Intra-European postdoctoral fellowship (awarded but declined) 2005 - EMBO long-term postdoctoral fellowship 2001 - Boehringer Ingelheim Fonds PhD scholarship (awarded but declined) 2000 - Fellowship of TEMPRA PECO program of Rhone-Alpes Region, France • TEACHING ACTIVITIES Since 2011 UJF Grenoble, Master 2 course on structural biology - lecture on experimental phasing. 2012 - 2013 EMBL Predoc course - lecture on “Readers and writers of the epigenetic landscape”. • ORGANISATION OF SCIENTIFIC MEETINGS 2013, 2015 Co-organiser of the “Signalling Through Chromatin” international symposium in Grenoble Since 2012 Co-organiser of regular meetings of the Chromatin, Transcription and Epigenetics community of Grenoble. • INSTITUTIONAL RESPONSIBILITIES Since 2016 Co-responsible of the Molecular Medicine research axis at the IBS 2009 - 2015 Faculty member - EMBL 2009 - 2015 Chairing lab committee meetings of the EMBL Grenoble • OTHER SCIENTIFIC ACTIVITIES 2011 - 2016 Editor of the online protocol database of the FP7 EU Network of Excellence ‘Epigenesys’. 2009 - 2013 Provide support to beamline users of the European Synchrotron Radiation Facility (ESRF) • COMMISSIONS OF TRUST 2016 External Grant Evaluator, European Research Council (ERC) 2014 External Grant Evaluator, National Science Center, Poland. Since 2012 Reviewer for PLoS ONE, RNA Biology, Journal of Structural Biology. • MAJOR COLLABORATIONS Asifa Akhtar - Max Planck Institute of Immunobiologie and Epigenetics, Freiburg, Germany. Functional analysis of MOF-containing complexes Bernard de Massy - Institut de Génétique Humaine, Montpellier, France. Functional analysis of PRDM9. • PRESENTATIONS - Central European Institute of Technology (CEITEC), Brno, Czech Republic, 2016, invited speaker - Instruct Workshop on Molecular interactions, Grenoble, 2015, invited speaker - Epigenesys Kick-Off meeting, Paris, France, 2010, invited speaker - VIZIER/Spine2Complexes Joint Workshop on Structural Virology, Vienna, Austria, 2008, invited speaker - 24th European Crystallographic meeting, Marrakech, Morocco, 2007, invited speaker - Structure, Function and Dynamics of RNA-protein Complexes, Gottingen, Germany, 2003, selected speaker ! 5 • SELECTED PUBLICATIONS * Corresponding author Dias, J., Nguyen, N., Georgiev, P., Gaub, A., Brettschneider, J., Cusack, S., Kadlec,