Kinetochore-Driven Control of Meiotic DNA Break Formation and Recombination at Centromere-Proximal Regions

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Kinetochore-Driven Control of Meiotic DNA Break Formation and Recombination at Centromere-Proximal Regions Kinetochore-driven control of meiotic DNA break formation and recombination at centromere-proximal regions Inaugural-Dissertation zur Erlangung des Doktorgrades Dr. rer. nat. der Fakultät für Biologie an der Universität Duisburg-Essen vorgelegt von Lisa-Marie Kuhl aus Witten durchgeführt am Max Planck Institut für molekulare Physiologie Abteilung für mechanistische Zellbiologie Februar 2018 Die der vorliegenden Arbeit zugrunde liegenden Experimente wurden am Max Planck Institut für molekulare Physiologie in der Abteilung für mechanistische Zellbiologie durchgeführt. 1. Gutachter: Prof. Dr. Andrea Musacchio 2. Gutachter: Prof. Dr. Stefan Westermann Vorsitzender des Prüfungsausschusses: Prof. Dr. Hemmo Meyer Tag der mündlichen Prüfung: 13. April 2018 Diese Dissertation wird über DuEPublico, dem Dokumenten- und Publikationsserver der Universität Duisburg-Essen, zur Verfügung gestellt und liegt auch als Print-Version vor. DOI: 10.17185/duepublico/46030 URN: urn:nbn:de:hbz:464-20190418-114218-2 Alle Rechte vorbehalten. In the context of this doctoral work, the following article was published: - Vincenten, N., Kuhl, LM., Lam, I., Oke, A., Kerr, ARW., Hochwagen, A., Fung, J., Keeney, S., Vader, G., Marston, AL. (2015). The kinetochore prevents centromere- proximal crossover recombination during meiosis. Elife 4: e10850 Index I Content Content………………………………..………………………………………………...........I List of Figures ........................................................................................................... V List of Tables .......................................................................................................... VIII List of Abbreviations ............................................................................................... IX 1 Introduction .......................................................................................................... 1 1.1 An overview of meiosis: Similarities and differences from mitosis .......... 1 1.1.1 Cell cycle phases ....................................................................................... 3 1.1.2 G1 phase .................................................................................................... 4 1.1.3 S phase ...................................................................................................... 4 1.1.4 G2/ prophase I ............................................................................................ 5 1.1.5 Meiosis I and meiosis II .............................................................................. 8 1.1.6 Cyclin dependent kinases and Dbf4/ Cdc7 kinase ................................... 10 1.1.7 Checkpoints .............................................................................................. 11 1.2 An overview of meiotic recombination in S. cerevisiae ........................... 12 1.2.1 Meiotic recombination: From DSB formation to inter-homolog repair ........ 12 1.2.2 Non-random genome-wide distribution of meiotic recombination events .. 15 1.3 Centromeric and pericentromeric regions ................................................ 18 1.3.1 Centromeres and pericentromeres are cold regions for meiotic DSB formation and recombination .............................................................................. 19 1.3.2 Centromere- and pericentromere-associated proteins ............................. 22 1.4 The kinetochore: Composition and function in S. cerevisiae .................. 26 1.4.1 The Ctf19 complex ................................................................................... 29 1.5 Objectives ..................................................................................................... 32 2 Materials and Methods ....................................................................................... 34 2.1 Materials ........................................................................................................ 34 2.1.1 Chemicals and Reagents ......................................................................... 34 2.1.2 Enzymes and commercially prepared master mixes ................................ 35 2.1.3 Kits ........................................................................................................... 36 2.1.4. Laboratory instruments and supplies ....................................................... 37 2.1.5 Antibodies ................................................................................................. 39 2.1.6 Buffers and solutions. ............................................................................... 40 Index II 2.1.7 Media. ....................................................................................................... 44 2.1.8 Yeast strains. ............................................................................................ 45 2.1.9 Synthetic oligonucleotides. ....................................................................... 45 2.1.10 Plasmids. ............................................................................................... 45 2.1.11 Online Tools. .......................................................................................... 46 2.1.12 Software ................................................................................................ 46 2.2 Methods ........................................................................................................ 48 2.2.1 Growth and maintenance of S. cerevisiae ................................................ 48 2.2.1.1 Growth conditions of yeast strains ...................................................... 48 2.2.1.2 Meiotic cell cycle synchronization ....................................................... 48 2.2.1.3 Yeast stock preservation ..................................................................... 49 2.2.1.4 Yeast cell growth assay ...................................................................... 49 2.2.2 Construction of yeast strains .................................................................... 49 2.2.2.1 Competent yeast cells ......................................................................... 49 2.2.2.2 Yeast transformation ........................................................................... 50 2.2.2.3 Diploid yeast strain creation ................................................................ 50 2.2.3 Methods of DNA analysis ......................................................................... 51 2.2.3.1 Polymerase Chain Reaction (PCR) ..................................................... 51 2.2.3.2 Agarose gel electrophoresis ................................................................ 52 2.2.3.3 DNA extraction and purification ........................................................... 52 2.2.3.4 Gibson assembly ................................................................................. 52 2.2.3.5 Transformation of plasmid DNA into competent bacteria cells ........... 53 2.2.3.6 Colony PCR ........................................................................................ 53 2.2.3.7 Isolation of plasmid from Escherichia coli ........................................... 53 2.2.3.8 Determination of DNA concentration ................................................... 53 2.2.3.9 Sequencing ......................................................................................... 54 2.2.3.10 Real time quantitative PCR (qPCR) .................................................. 54 2.2.3.11 Southern Blot .................................................................................... 55 2.2.3.11.2 Digestion of genomic DNA ......................................................... 56 2.2.3.11.3 Southern blotting procedure ....................................................... 57 2.2.3.11.4 Southern blot hybridization and washing .................................... 57 2.2.3.11.5 Phosphorimaging ........................................................................ 58 2.2.3.12 Genomic DNA preparation from yeast for PCR-based genotyping ... 58 2.2.3.13 Analysis of the meiotic program by flow cytometry ........................... 59 Index III 2.2.4 Methods of protein analysis ...................................................................... 59 2.2.4.1 Western blot ........................................................................................ 59 2.2.4.2 Yeast whole cell extract for Western blotting using trichloroacetic acid ........................................................................................................................ 59 2.2.4.4 Western blotting procedure ................................................................. 61 2.2.4.5 Chromatin immunoprecipitation .......................................................... 62 2.2.4.6 Co-Immunoprecipitation ...................................................................... 63 2.2.5 Meiotic recombination, DNA double-strand breaks and spore analyses ... 64 2.2.5.1 Live cell reporter assay ....................................................................... 64 2.2.5.2 Sporulation efficiency and spore viability ............................................ 65 3 Results ................................................................................................................ 67 3.1 The Ctf19-C plays a role in controlling meiotic homologous recombination at pericentromeres ..................................................................... 67 3.2 The Ctf19-C minimizes meiotic DSB formation at pericentromeres ....... 72 3.3 CEN1-proximal DSB formation is reduced by the Ctf19-C
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