The role and regulation of histone H2B monoubiquitination during tumorigenesis Dissertation for the award of the degree “Doctor rerum naturalium (Dr. rer. nat.)“ Division of Mathematics and Natural Sciences of the Georg-August-Universität Göttingen submitted by Theresa Gorsler born in Leinefelde Hamburg, 2013 Members of the Thesis Committee: Prof. Dr. Steven A. Johnsen (Reviewer) Department of Tumor Biology University Medical Center Hamburg-Eppendorf, Hamburg Prof. Dr. Holger Reichardt (Reviewer) Department of Cellular and Molecular Immunology University of Göttingen Medical School, Göttingen Prof. Dr. Dieter Kube Department of Immunology and Experimental Oncology University of Göttingen Medical School, Göttingen Date of the oral examination: 3rd of june 2013 Affidavit I hereby declare that the PhD thesis entitled “The role and regulation of histone H2B monoubiquitination during tumorigenesis” has been written independently and with no other sources and aids than quoted. _____________________________ Theresa Gorsler April, 2013 Hamburg Table of Contents Abbreviations ............................................................................................... I List of Figures ............................................................................................ VI Summary ................................................................................................. VIII 1 Introduction .............................................................................................. 1 1.1 Chromatin structure ................................................................................................ 1 1.2 Histone modifications ............................................................................................. 2 1.2.1 “Histone code” ................................................................................................. 4 1.2.2 Misregulation of histone modifications ............................................................. 5 1.2.3 Histone monoubiquitination .............................................................................. 6 1.2.3.1 Histone H2Bub1 .................................................................................................................... 7 1.3 Functional role of H2B monoubiquitination ............................................................. 9 1.3.1 H2Bub1 and transcription ................................................................................ 9 1.3.2 Cellular functions of the H2Bub1 in yeast ...................................................... 10 1.3.3 The role of H2Bub1 in higher eukaryotes ....................................................... 11 1.3.4 Genome-wide distribution of H2Bub1 ............................................................ 13 1.3.5 H2Bub1 and its regulation in human cancer .................................................. 14 1.4 Histone H2B deubiquitination ............................................................................... 14 1.4.1 The SAGA complex ....................................................................................... 15 1.4.1.1 USP22 as the main deubiquitinase for H2B ........................................................................ 16 1.4.1.2 The SAGA deubiquitination module .................................................................................... 17 1.4.1.3 Other H2Bub1 deubiquitinases ........................................................................................... 18 1.5 Nucleoli and stress conditions .............................................................................. 19 1.5.1 Nucleoli .......................................................................................................... 19 1.5.2 Nucleolar reaction to stress ........................................................................... 19 1.5.3 Nucleoli and JNK signaling ............................................................................ 20 1.5.4 AMPK signaling in tumorigenesis and tumor metabolism .............................. 21 2 Materials ................................................................................................ 22 2.1 Technical equipment ............................................................................................ 22 2.2 Consumable materials ......................................................................................... 23 2.3 Chemicals ............................................................................................................ 24 2.3.1 General chemicals ......................................................................................... 24 2.3.2. Inhibitors ....................................................................................................... 28 2.4 Kits and reagents ................................................................................................. 28 2.5 Nucleic acids ........................................................................................................ 29 2.5.1 Vectors and expression constructs ................................................................ 29 2.5.2 Oligonucleotides ............................................................................................ 29 2.5.2.1 siRNA oligonucleotides ........................................................................................................ 29 2.5.2.2 RT-PCR primers .................................................................................................................... 31 2.5.2.3 qPCR primers ....................................................................................................................... 31 2.5.2.4 ChIP primers ........................................................................................................................ 32 2.5.2.4 Primers for ChIP-seq library preparation ............................................................................ 32 2.6 Proteins ................................................................................................................ 33 2.6.1 Molecular weight standards ........................................................................... 33 2.6.2 Enzymes ........................................................................................................ 33 2.6.3 Antibodies ...................................................................................................... 34 2.6.3.1 Primary antibodies .............................................................................................................. 34 2.6.3.2 Secondary antibodies .......................................................................................................... 35 2.7 Cells ..................................................................................................................... 35 2.7.1 Bacteria cells ................................................................................................. 35 2.7.2 Eukaryotic cell lines ....................................................................................... 35 2.8 Buffers and solutions ............................................................................................ 36 2.9 Software ............................................................................................................... 42 3 Methods................................................................................................. 43 3.1 Cell culture ........................................................................................................... 43 3.1.1 Culturing cells ................................................................................................ 43 3.1.2 Reverse-transfection with siRNA ................................................................... 43 3.1.3 Colony formation assay ................................................................................. 43 3.1.4 Migration assay .............................................................................................. 44 3.1.5 Measurement of DNA of single cells by flow cytometry ................................. 44 3.1.6 ATP determination assay ............................................................................... 45 3.2. Molecular biology ................................................................................................ 45 3.2.1 RNA isolation ................................................................................................. 45 3.2.2 cDNA synthesis.............................................................................................. 45 3.2.3 Quantitative real-time PCR ............................................................................ 46 3.2.4 Microarray analyses ....................................................................................... 46 3.2.5 Chromatin immunoprecipitation (ChIP) .......................................................... 48 3.2.6 Chromatin immunoprecipitation-sequencing (ChIP-Seq) ............................... 49 3.3 Protein biochemistry ............................................................................................. 53 3.3.1 SDS-PAGE .................................................................................................... 53 3.3.2 Western blot analysis ..................................................................................... 53 3.3.3 In vitro deubiquitination assay ........................................................................ 53 3.3.4 Immunohistochemistry on paraffin sections ..................................................