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Identification and Characterisation of Mybbp1a As a Regulator of Rrna Synthesis

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Identification and Characterisation of Mybbp1a As a Regulator of Rrna Synthesis Dissertation zur Erlangung des Doktorgrades der Fakultät für Biologie der Ludwig-Maximilians-Universität München Identification and Characterisation of Mybbp1a as a Regulator of rRNA Synthesis Julia Hochstatter aus München 2011 Ehrenwörtliche Versicherung Ich versichere hiermit ehrenwörtlich, dass die vorgelegte Dissertation von mir selbständig und ohne unerlaubte Hilfe angefertigt ist. München, den 01.06.2011 Julia Hochstatter Erklärung Hiermit erkläre ich, dass die Dissertation nicht ganz oder in wesentlichen Teilen einer anderen Prüfungskommission vorgelegt worden ist. Ich habe mich nicht anderweitig einer Doktorprüfung unterzogen und ich habe zu keinem früheren Zeitpunkt versucht, eine Dissertation einzureichen oder mich der Doktorprüfung zu unterziehen. München, den 01.06.2011 Julia Hochstatter Dissertation eingereicht am: 01. Juni 2011 1. Gutachter: Prof. Dr. Peter Becker 2. Gutachterin: Prof. Dr. Elisabeth Weiß Tag der mündlichen Prüfung: 18.07.2011 Veröffentlichungen in Fachzeitschriften Teile bzw. Beiträge der vorliegenden Arbeit wurden in folgenden Artikel veröffentlicht: Julia Hochstatter, Attila Németh, Michael Hölzel, Michaela Rohrmoser, Lothar Schermelleh, Heinrich Leonhardt, Rebecca Keough, Thomas J. Gonda, Axel Imhof, Dirk Eick and Gernot Längst Mybbp1a is Involved in the Regulation of rRNA Gene Transcription and pre-rRNA Processing submitted Hölzel M, Orban M, Hochstatter J, Rohrmoser M, Harasim T, Malamoussi A, Kremmer E, Längst G, Eick D. Defects in 18 S or 28 S rRNA processing activate the p53 pathway. J Biol Chem. 2010 Feb 26;285(9):6364-70. Epub 2010 Jan 7. Für Moritz und Franz Acknowledgements First, I would like to thank my supervisor Prof. Dr. Gernot Längst for giving me the opportunity to work on an exciting project in a great team. I am grateful for his constant advice, his creative input and long-lasting support. Danke dir! I am very grateful to Prof. Dr. Peter Becker for supporting this thesis work by offering an inspiring and exceptional environment at the institute. Thank you for reviewing the PhD thesis and supervision. As well, I am thankful to Prof. Dr. Elisabeth Weiß for reviewing my PhD thesis. Furthermore, I would like to thank Michi Hölzel and Prof. Dr. Dirk Eick for the conjoint work, intensive discussions and helpful suggestions. Special thanks go to the original Längst group: Ralf Strohner, Attila Németh, Karoline Dachauer and Anna Schrader for sharing protocols and buffers, extensive discussions in and around the institute and the great atmosphere. I would like to thank all present and former lab members for permanent help, sharing expertise and the nice and constructive lab environment. Thanks to Andreas Hochheimer for IP advice and music, Tobias Straub for statistical, computer-wise and medical first-aid, Axel Imhof, Lars Israel and Tilman Schlunk for mass spectrometry analysis, Alexander Brehm and Anton Eberharter for helpful discussions, Christina Schwarzlose for tissue culture support, Axel Imhof and the histone modification group for keeping me close to science during the past 4 years, Michi Korenjak for talking about extracts and together with Angie Mitterweger, Matthias Prestel, Sabina, Gregor Gilfillan and Jörn Böke for setting up the Wildschönau tradition. Im Besonderen möchte ich meinen Eltern Barbara und Bernd Hochstatter für ihre vielfältige und andauernde Unterstützung danken, meinen Geschwistern Iris und Matthias für großen Rückhalt. Mein Dank gilt Breda und Siegwart Groth für all ihre Hilfe und den schönsten Ausblick aus einem Arbeitszimmer. Innig danke ich Martin und unseren Söhnen Moritz und Franz für ihr Verständnis, die Unterstützung und große Freude. Table of Contents i Table of contents 1 Summary ........................................................................................................................ 1 2 Introduction.................................................................................................................... 3 2.1 The ribosomal RNA genes ............................................................................................ 3 2.1.1 The nucleolus - the site of ribosome biogenesis......................................................... 3 2.1.2 The organisation of mammalian rRNA genes ............................................................. 5 2.1.3 The two different chromatin states of the rRNA genes ............................................... 6 2.1.4 Epigenetic and topological features of active and inactive rRNA genes ..................... 8 2.2 rRNA gene expression by RNA polymerase I.............................................................. 11 2.2.1 Initiation of rRNA gene transcription......................................................................... 11 2.2.2 rRNA gene transcription elongation.......................................................................... 13 2.2.3 Termination of rRNA gene transcription ................................................................... 14 2.3 rRNA processing and ribosome assembly................................................................... 16 2.3.1 The cleavage events of the rRNA processing pathway ............................................ 16 2.3.2 Co-transcriptional processing and ribosome assembly............................................. 18 2.4 Co-ordination of ribosome biogenesis ......................................................................... 20 2.4.1 Co-regulation of rRNA gene transcription, processing and ribosome assembly........ 20 2.4.2 Adapting ribosome biogenesis to the metabolic state of the cell............................... 22 2.4.3 Feed-back mechanisms from ribosome biogenesis to cellular proliferation .............. 24 2.5 The Myb-binding protein 1a ........................................................................................ 25 2.5.1 Characteristics and structural features of Mybbp1a.................................................. 25 2.5.2 Functional properties of Mybbp1a ............................................................................ 26 2.6 Objectives ................................................................................................................... 29 3 Materials and Methods ................................................................................................ 30 3.1 Material....................................................................................................................... 30 3.1.1 Solutions, buffers and media.................................................................................... 30 3.1.2 Consumables and equipment................................................................................... 32 3.1.3 Antibodies ................................................................................................................ 33 3.1.4 Vectors..................................................................................................................... 34 3.1.5 Oligonucleotides ...................................................................................................... 35 3.1.6 siRNA sequences .................................................................................................... 35 3.1.7 Bacteria strains and cell lines................................................................................... 35 3.2 Methods...................................................................................................................... 37 3.2.1 Generation of a mouse Flag-RPA116 expression construct ..................................... 37 3.2.2 Cell culture and generation of a MB III cells stably expressing Flag-RPA116 ........... 37 3.2.3 DNA transfection of mammalian cells....................................................................... 37 3.2.4 Extract preparation................................................................................................... 38 Table of Contents ii 3.2.4.1 Nuclear extract from MB III and HEK293T cells..................................................... 38 3.2.4.2 Whole Cell extract from MBIII cells........................................................................ 38 3.2.4.3 Nuclear extract from HeLa cells ............................................................................ 39 3.2.5 Immunopurification of proteins ................................................................................. 39 3.2.6 Co-immunoprecipitation of Flag-Mybbp1a-associated factors .................................. 39 3.2.7 Immunofluorescent staining and image capture ....................................................... 40 3.2.7.1 RNA-dependent-localisation of proteins ................................................................ 40 3.2.7.2 BrdU labeling of newly synthesised DNA............................................................... 40 3.2.8 siRNA-mediated protein depletion............................................................................ 40 3.2.9 Analysis of the rRNA precursor and β-actin mRNA by quantitative real-time PCR ... 41 3.2.9.1 Cellular RNA extraction ......................................................................................... 41 3.2.9.2 Reverse transcription of cellular RNA.................................................................... 41 3.2.9.3 Quantitative PCR .................................................................................................. 41 3.2.10 Metabolic labeling of nascent RNA in HeLa cells ..................................................... 42 3.2.11 Proliferation assay ..................................................................................................
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