Comparison of genome-wide nucleosome positioning mechanisms in Schizosaccharomyces pombe and Saccharomyces cerevisiae [Elektronische Ressource] / Alexandra Lantermann

Alexandra Lantermann

Sujets

• Biologie

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2010
• Nombre de lectures: 40
• Langue: Deutsch
• Poids de l'ouvrage: 3 Mo

Extrait

Dissertation zur Erlangung des Doktorgrades
der Fakultät für Biologie
der Ludwig-Maximilians-Universität München







Comparison of Genome-Wide Nucleosome Positioning
Mechanisms in Schizosaccharomyces pombe and
Saccharomyces cerevisiae




Alexandra Lantermann

München
20. Mai 2010


































Dissertation eingereicht am: 20. Mai 2010
Mündliche Prüfung am: 20. Juli 2010

1. Gutachter: Prof. Dr. Peter Becker
2. Gutachter: Prof. Dr. Stefan Jentsch
3. Gutachter: Prof. Dr. Dario Leister
4. Gutachter: Prof. Dr. Michael Boshart
5. Gutachter: Prof. Dr. Angelika Böttger
6. Gutachter: Prof. Dr. Dirk Eick




Ehrenwörtliche Versicherung


Ich versichere hiermit ehrenwörtlich, dass die vorgelegte Dissertation von mir selbständig und
ohne unerlaubte Hilfe angefertigt wurde.


München, den ……………………………… …..………………………………………….
(Alexandra Lantermann)


























Erklärung


Hiermit erkläre ich, dass ich mich nicht anderweitig einer Doktorprüfung ohne Erfolg
unterzogen habe.


München, den ……………………………… …..………………………………………….
(Alexandra Lantermann)













































Wesentliche Teile dieser Arbeit sind in folgenden Publikationen veröffentlicht:





Lantermann, A., T. Straub, A. Stralfors, G. C. Yuan, K. Ekwall and P. Korber (2010).
Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning
mechanisms distinct from those of Saccharomyces cerevisiae. Nat Struct Mol Biol 17(2):
251-257.


Lantermann, A., A. Stralfors, F. Fagerstrom-Billai, P. Korber and K. Ekwall (2009). Genome-
wide mapping of nucleosome positions in Schizosaccharomyces pombe. Methods 48(3): 218-
225.












































































Diese Arbeit ist Mama und Papa, Christiane und Ulf gewidmet.


Acknowledgements

I would like to thank


Dr. Philipp Korber for giving me the opportunity to join his group, to work on this great
project, for his constant support and advice throughout the thesis, and for always finding time
for very stimulating discussions,

Prof. Dr. Peter Becker for following up my work and constant support, for taking over the
role of an official supervisor, and for his big contribution to a stimulating scientific
environment and nice atmosphere in the lab,

Prof. Dr. Stefan Jentsch for being the second member of my PhD committee,

Dr. Tobias Straub, for all his support with bioinformatical and statistical data analysis and
interpretation, for his patience, for teaching me R, and for very helpful discussions,

Prof. Dr. Guo-Cheng Yuan for N-score model calculations and testing the HMM,

Prof. Dr. Karl Ekwall for collaboration on this project, stimulating discussions, and providing
strains and data sets,

Annelie Strålfors for teaching me the Tiling Analysis Software, sending S. pombe strains and
bringing my samples to the Affymetrix facility,

Prof. Hiten Madhani and Ramón Ramos Barrales for providing S. pombe strains,

Natalie Dutrow for advice on the analysis of transcriptome data,

Dr. Sandra Hake and Prof. Dr. Axel Imhof for being in my thesis advisory committee and for
very helpful discussions,

Dr. Felix Müller-Planitz for teaching me the basics of MATLAB,

Edith Müller and Carolin Brieger from the secretary for being so well organized, helpful, and
for sending away my Stockholm packages,

Dorle Blaschke, Franziska Ertel and Christian Wippo for teaching me their technical
expertise, for fun in the lab, and for contributing to a great working atmosphere,

The whole North Lab and all the people from the molecular biology department who made
work every day much more fun,

My parents and my sister for constant familiar support,

Ulf and my friends for constant support and non-constant distraction.



Table of contents


Table of contents

Summary ......................................................................................................................................... 1
Zusammenfassung.......................................................................................................................... 2
1 Introduction............................................................................................................................ 3
1.1 Basic levels of chromatin organization in eukaryotes ..................................................... 3
1.2 Mechanisms for regulation of chromatin structure.......................................................... 5
1.3 Nucleosome positioning .................................................................................................. 7
1.3.1 Methods to map nucleosomes ..................................................................................... 9
1.3.2 Outcome of genome-wide nucleosome occupancy maps.......................................... 10
1.3.3 Mechanisms of nucleosome positioning ................................................................... 11
1.3.3.1 The role of intrinsic DNA sequence features in nucleosome positioning......... 12
1.3.3.2 The role of trans-factors in nucleosome positioning......................................... 16
1.4 Aims of this work .......................................................................................................... 19
2 Materials and methods ........................................................................................................ 20
2.1 Materials ........................................................................................................................ 20
2.1.1 Chemicals .................................................................................................................. 20
2.1.2 Enzymes .................................................................................................................... 21
2.1.3 Other materials .......................................................................................................... 21
2.1.4 Oligonucleotides and plasmids.................................................................................. 22
2.1.4.1 Oligonucleotides ............................................................................................... 22
2.1.4.2 Plasmids ............................................................................................................ 23
2.1.5 Bacteria and yeast strains .......................................................................................... 23
2.1.5.1 E. coli strains..................................................................................................... 23
2.1.5.2 S. pombe strains................................................................................................. 23
2.1.5.3 S. cerevisiae strains ........................................................................................... 24
2.2 Media, buffers and solutions.......................................................................................... 24
2.2.1 Media......................................................................................................................... 24
2.2.1.1 Media for E. coli ............................................................................................... 24
2.2.1.2 S. pombe 24
2.2.1.3 Media for S. cerevisiae...................................................................................... 25
2.2.2 Buffers and solutions 25
2.3 General methods for working with DNA and RNA ...................................................... 30
2.3.1 Horizontal and vertical agarose gel electrophoresis of DNA .................................... 30
2.3.2 Polymerase chain reaction (PCR).............................................................................. 30
2.3.3 DNA purification by phenol/chl