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Untersuchung Des Metabolismus Nicht-Kanonischer DNA-Basen In Dissertation zur Erlangung des Doktorgrades der Fakultät für Chemie und Pharmazie der Ludwig-Maximilians-Universität München Untersuchung des Metabolismus nicht-kanonischer DNA-Basen in embryonalen Stammzellen Angie Gabriele Kirchner aus Ulm, Deutschland 2020 Erklärung Diese Dissertation wurde im Sinne von § 7 der Promotionsordnung vom 28. November 2011 von Herrn Prof. Dr. Thomas Carell betreut. Eidesstattliche Versicherung Diese Dissertation wurde selbstständig und ohne unerlaubte Hilfe erarbeitet. München, den 09.01.2020 ......................................... Angie G. Kirchner Dissertation eingereicht am: 09.01.2020 1. Gutachter: Prof. Dr. Thomas Carell 2. Gutachterin: Dr. Stefanie Kellner Mündliche Prüfung am: 31.01.2020 „I am just a child who has never grown up. I still keep asking these ‘how’ and ‘why’ questions. Occasionally, I find an answer.” Stephen Hawking Teile dieser Arbeit wurden in folgenden Journalen oder auf Fachkonferenzen publiziert: Publikationen F. Spada, S. Schiffers, A. Kirchner, Y. Zhang, O. Kosmatchev, E. Korytiakova, R. Rahimoff, C. Ebert, T. Carell, Oxidative and non-oxidative active turnover of genomic methylcytosine in distinct pluripotent states, bioRxiv 2019, 846584, 10.1101/846584. K. Iwan*, R. Rahimoff*, A. Kirchner*, F. Spada*, A. S. Schröder, O. Kosmatchev, S. Ferizaj, J. Steinbacher, E. Parsa, M. Müller, T. Carell, 5-Formylcytosine to cytosine conversion by C-C bond cleavage in vivo, Nat. Chem. Biol. 2018, 14, 72-78, 10.1038/nchembio.2531. R. Rahimoff*, O. Kosmatchev*, A. Kirchner*, T. Pfaffeneder, F. Spada, V. Brantl, M. Müller, T. Carell, 5-Formyl- and 5-carboxydeoxycytidines do not cause accumulation of harmful repair intermediates in stem cells, J. Am. Chem. Soc. 2017, 139, 10359-10364, 10.1021/jacs.7b04131. M. Su, A. Kirchner, S. Stazzoni, M. Müller, M. Wagner, A. Schröder, T. Carell, 5-Formylcytosine could be a semipermanent base in specific genome sites, Angew. Chem. Int. Ed. Engl. 2016, 55, 11797-11800, 10.1002/anie.201605994. * Beitrag der Autoren zu gleichen Teilen. Konferenzbeiträge The 43rd FEBS Congress – Biochemistry Forever, The Czech Society for Biochemistry and Molecular Biology, Prague, Czech Republic (2018) – Posterpräsentation: “Studies towards a C-C bond cleavage of 5-formyl-2’-deoxycytidine in mammalian cells” SFB 1309 Meeting – Chemical Biology of Epigenetic Modifications, Ludwig-Maximilians-University, Munich, Germany (2017) – Posterpräsentation: “Investigation of enzymes involved in the C-C bond cleavage of 5-formyldeoxycytidine” Frontiers in Epigenetic Chemical Biology, The Royal Society, London, United Kingdom (2017) – Posterpräsentation: “A novel reagent for the detection and quantification of base excision repair intermediates” Danksagung An erster Stelle möchte ich meinem Doktorvater Prof. Dr. Thomas Carell für die herausfordernde Themenstellung und die exzellenten Arbeitsbedingungen danken. Ebenso danke ich dir für deine stete Unterstützung und das entgegengebrachte Vertrauen in meine Arbeit. Dr. Stefanie Kellner danke ich ganz herzlich für die Übernahme des Koreferats. Allen weiteren Mitgliedern der Prüfungskommission Prof. Dr. Stylianos Michalakis, Prof. Dr. Lena Daumann, Dr. Dietmar Martin und Prof. Dr. Konstantin Karaghiosoff danke ich vielmals für ihre Mitwirkung an der mündlichen Prüfung. Frau Slava Gärtner danke ich für ihre Hilfe in allen organisatorischen Angelegenheiten. Dr. Fabio Spada möchte ich für seine fachliche, wie auch persönliche Unterstützung und guten Ratschläge in allen Phasen meiner Promotion herzlichst danken. Deine Begeisterung für die Stammzellbiologie und die vielen lehrreichen Unterhaltungen haben mich zum Gelingen dieser Arbeit motiviert. Dr. Markus Müller gebührt großer Dank für seine bedingungslose Hilfsbereitschaft in allen Belangen. Ebenso danke ich dir für die Ermutigung Ergebnisse kritisch zu hinterfragen und die angeregten wissenschaftlichen Diskussionen. Dank dir habe ich mich nicht nur persönlich weiterentwickelt, sondern auch meine graphischen Fähigkeiten verbessert. Ein besonderer Dank geht auch an alle Korrekurleser Dr. Sarah Schiffers, Eva Korytiakovà, Dr. Katharina Iwan, Franziska Traube, Dr. Fabio Spada und Dr. Markus Müller. Großer Dank gebührt meinen beiden Lieblingsmitstreitern Dr. René Rahimoff und Dr. Katharina Iwan. Unsere gute Zusammenarbeit hat den großen Erfolg unserer Themen erst möglich gemacht. Ich werde eure Effizienz, die angeregten Diskussionen und eure unerschütterliche Begeisterung für die Wissenschaft vermissen. Auch dem „BabySafe-Lab“, Johanna Bretzler mit Anna sowie Franziska Traube mit Malin (alias Erwin), möchte ich für die gute Stimmung, die lustigen Momente und die gute Arbeitsatmosphäre danken. Ich kann mich glücklich schätzen so tolle Laborkolleginnen gehabt zu haben. Franziska Traube leider hatten wir nie die Gelegenheit zusammen die Weltherrschaft zu erobern, aber es wäre großartig geworden - und wer weiß, was die Zukunft bringt! Meinen QQQ-Ladies Dr. Jessica Steinbacher, Dr. Olesea Kosmatchev, Dr. Sarah Schiffers und Dr. Katharina Iwan danke ich für die Prozessierung und Auswertung unzähliger DNA-Proben. Herzlichst möchte ich mich auch bei Kerstin Kurz, Kristof Hufnagel und Luis de la Osa de la Rosa für die große Hilfe bei der täglichen Laborarbeit bedanken. Ohne euren Einsatz bei der DNA-Isolation, in der Zellkultur oder dem Probenverdau wäre vieles nicht so reibungslos verlaufen. Ebenfalls möchte ich mich bei der „Bärenhöhle“ Dr. Sidney Becker, Dr. Mirko Wagner, Dr. Katharina Iwan, Dr. Michael Stadlmeier, Dr. René Rahimoff und Dr. Nada Raddaoui für die freundliche Aufnahme ins Team bedanken. Es war eine schöne Zeit mit euch und ein toller Ausklang meiner Promotion. An dieser Stelle möchte ich mich bei meinen Praktikanten und Masteranden Shqiponja Ferizaj, Peyton Randoplh, David Schmidl und Ewelina Kamińska für ihre Unterstützung und wissenschaftlichen Diskussionen bedanken. Es hat mir unglaublich viel Spaß gemacht, euch zu betreuen und euren wissenschaftlichen und persönlichen Fortschritt mitzuerleben. Ich wünsche euch viel Erfolg und alles Gute für eure Zukunft! Ewelina Kamińska es freut mich sehr so eine motivierte und würdige Nachfolgerin zu haben - ich bin mir sicher du wirst alle Herausforderungen meistern! Auch allen weiteren Mitgliedern der Arbeitsgruppe möchte ich für die tolle Arbeitsatmosphäre und den guten Zusammenhalt danken. Viele Kollegen aus der Arbeitsgruppe konnte ich in dieser Zeit als Freunde gewinnen. Ich bin sehr froh euch hier kennengelernt zu haben und blicke auf unzählige lustige Abende mit euch beim Kochen, beim „Topmodeln“, im Biergarten oder bei Mottopartys zurück. Auch meinen Freunden außerhalb der Uni möchte ich für ihre Unterstützung, Geduld und ihr Verständnis an langen Arbeitstagen danken. Céline Kreiser und Carina Brosche herzlichen Dank für die Korrektur meiner Arbeit – auch wenn ihr fachfremd seid, habt ihr tolle Arbeit geleistet! Zum Schluss gilt mein herzlichster Dank meinen Eltern, die mich schon mein ganzes Leben begleiten und unterstützen. Ihr habt nie die Geduld und den Glauben an mich verloren und mir stets den nötigen Rückhalt geboten. Meinem Freund, Dr. Dominik Leitz, danke ich für seine Unterstützung, Liebe und guten Ratschläge. Ich hätte diese Zeit ohne dich nicht so gut gemeistert und bin dankbar, dich an meiner Seite zu haben. Inhaltsverzeichnis Zusammenfassung ................................................................................................................................... I Summary ................................................................................................................................................. V 1 Einleitung ........................................................................................................................................ 1 1.1 Zelluläre Differenzierung und Epigenetik .............................................................................. 1 1.2 Stammzellen als Modell der frühen Entwicklung .................................................................. 4 1.2.1 Gewinnung der pluripotenten Stammzellen ..................................................................... 4 1.2.2 Naïve und primed Pluripotenz ........................................................................................... 6 1.3 Epigenetische Regulation ...................................................................................................... 9 1.3.1 Chromatinstruktur und Histonmodifikationen ................................................................. 9 1.3.2 Nicht-kodierende RNA .................................................................................................... 11 1.4 DNA-Methylierung .............................................................................................................. 12 1.4.1 DNA-Methyltransferasen ................................................................................................ 13 1.4.2 Dynamik in der zellulären Entwicklung ........................................................................... 15 1.5 Tet-vermittelte Bildung der oxidierten mdC-Derivate ........................................................ 16 1.5.1 5-Hydroxymethyl-2´-desoxycytidin ................................................................................. 17 1.5.2 5-Formyl-2´-desoxycytidin und 5-Carboxyl-2´-desoxycytidin .......................................... 18 1.6 DNA-Demethylierung .......................................................................................................... 20 1.6.1 Passive DNA-Demethylierung
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