Molecular mechanism of dBigH1 action Miloš Tatarski ADVERTIMENT. La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del servei TDX (www.tdx.cat) i a través del Dipòsit Digital de la UB (diposit.ub.edu) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei TDX ni al Dipòsit Digital de la UB. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a TDX o al Dipòsit Digital de la UB (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora. ADVERTENCIA. La consulta de esta tesis queda condicionada a la aceptación de las siguientes condiciones de uso: La difusión de esta tesis por medio del servicio TDR (www.tdx.cat) y a través del Repositorio Digital de la UB (diposit.ub.edu) ha sido autorizada por los titulares de los derechos de propiedad intelectual únicamente para usos privados enmarcados en actividades de investigación y docencia. No se autoriza su reproducción con finalidades de lucro ni su difusión y puesta a disposición desde un sitio ajeno al servicio TDR o al Repositorio Digital de la UB. No se autoriza la presentación de su contenido en una ventana o marco ajeno a TDR o al Repositorio Digital de la UB (framing). Esta reserva de derechos afecta tanto al resumen de presentación de la tesis como a sus contenidos. En la utilización o cita de partes de la tesis es obligado indicar el nombre de la persona autora. WARNING. On having consulted this thesis you’re accepting the following use conditions: Spreading this thesis by the TDX (www.tdx.cat) service and by the UB Digital Repository (diposit.ub.edu) has been authorized by the titular of the intellectual property rights only for private uses placed in investigation and teaching activities. Reproduction with lucrative aims is not authorized nor its spreading and availability from a site foreign to the TDX service or to the UB Digital Repository. Introducing its content in a window or frame foreign to the TDX service or to the UB Digital Repository is not authorized (framing). Those rights affect to the presentation summary of the thesis as well as to its contents. In the using or citation of parts of the thesis it’s obliged to indicate the name of the author. Molecular mechanism of dBigH1 action Doctoral Thesis by Miloš Tatarski Programme of Biomedicine of the University of Barcelona Faculty of Pharmacy and Alimentation Sciences Barcelona, 2018 Thesis Director Mr. Ferran Azorín Marín, PhD Chromatin Structure and Function Group Institute for Research in Biomedicine (IRB), Barcelona Institute of Molecular Biology of Barcelona, CSIC Tutoress Mrs. Nieves Agell Jané, PhD School of Medicine, University of Barcelona (UB) Department of Cell Biology, Immunology and Neuroscience Doctoral Student Miloš Tatarski ii iii Acknowledgements iv First, I want to thank Ferran for letting me perform my thesis in his laboratory. During all this time you have been very supportive on a professional and personal level, I was lucky to learn a lot during my time in your group. People with such a love for science are rare, and I hope you will continue working in research for many more years. Thanks to all the group, I enjoyed working with all of you. Apart from having you as friends I could always count on your support and help during more difficult times of my thesis. Although those difficult times are very common in a thesis’ lifetime and they usually come together with serious doubts, I realize that the things I learned and the experience I made have added an important value to my person that will help me throughout my life. Thank you again for making it possible!! Thanks to the many friends I made during my time at the IRB. They fill my memories with countless moments of laughter and joy that I am already missing a lot! I will always remember you and the great time we had. I hope to stay in close contact with all of you, but unfortunately this is something that is not always easy to achieve… I wish you all the best for your future and if we don’t manage to stay in touch we will keep the memories that from time to time appear in our minds and make us laugh. And finally, I want to thank the city of Barcelona and its people. I consider myself very lucky to have spent an important part of my life here. v Table of Contents Acknowledgements .......................................................................................................................iv Table of Contents ......................................................................................................................vi List of Figures ................................................................................................................................ ix 1. INTRODUCTION ..................................................................................................................... 1 1.1. DNA in a living cell .............................................................................................................. 3 1.1.1. DNA condensation............................................................................................................... 3 1.1.2. Different types of chromatin ............................................................................................... 4 1.1.3. The nucleosome .................................................................................................................. 5 1.1.4. The core histones ................................................................................................................ 7 1.1.5. Core histone modifications ................................................................................................. 8 1.1.6. Histone variants ................................................................................................................ 10 1.2. Linker histone H1 ............................................................................................................. 11 1.2.1. Linker histone H1 structure ............................................................................................... 12 1.2.2. Linker histone H1 in Drosophila ........................................................................................ 13 1.2.3. Linker histone H1 modifications........................................................................................ 14 1.2.4. Linker histone H1 modifications in Drosophila ................................................................. 15 1.2.5. Functions of linker histone H1 .......................................................................................... 16 1.3. Embryonic and germline specific linker histone variants................................................. 17 1.3.1. Embryonic and germline specific linker histone dBigH1 ................................................... 19 1.3.2. The dBigH1 N-terminal domain ......................................................................................... 20 1.3.3. dBigH1 gets replaced by somatic H1 at cellularization ..................................................... 21 1.3.4. dBigH1 modifications ........................................................................................................ 22 1.3.5. dBigH1 stays in the primordial germ cells ......................................................................... 23 1.3.6. dBigH1 represses zygotic gene activation ......................................................................... 23 1.4. Chromatin remodelers and histone chaperones ............................................................. 24 1.4.1. The chromatin remodeler ACF1 ........................................................................................ 26 1.4.2. The histone chaperone NAP1 ............................................................................................ 28 1.5. Drosophila Melanogaster as a model organism .............................................................. 30 1.5.1. The Drosophila life cycle ................................................................................................... 31 1.5.2. The syncytial blastoderm .................................................................................................. 32 1.6. Spermatogenesis in Drosophila ........................................................................................ 34 1.6.1. The fusome ........................................................................................................................ 36 vi 1.7. Transcription in DREX ....................................................................................................... 37 1.7.1. In vitro transcription using HeLa nuclear extract .............................................................. 39 2. MATERIALS & METHODS ..................................................................................................... 41 2.1. Materials .......................................................................................................................... 43 2.1.1. Antibodies ......................................................................................................................... 43 2.1.2. Fly lines .............................................................................................................................