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University of Dundee DOCTOR of PHILOSOPHY Investigating The University of Dundee DOCTOR OF PHILOSOPHY Investigating the mechanisms of action of the SNF2-homolog protein Fun30 Mahmoud, Salma Awad Award date: 2011 Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 04. Oct. 2021 DOCTOR OF PHILOSOPHY Investigating the mechanisms of action of the SNF2-homolog protein Fun30 Salma Awad Mahmoud 2011 University of Dundee Conditions for Use and Duplication Copyright of this work belongs to the author unless otherwise identified in the body of the thesis. It is permitted to use and duplicate this work only for personal and non-commercial research, study or criticism/review. You must obtain prior written consent from the author for any other use. Any quotation from this thesis must be acknowledged using the normal academic conventions. It is not permitted to supply the whole or part of this thesis to any other person or to post the same on any website or other online location without the prior written consent of the author. Contact the Discovery team ([email protected]) with any queries about the use or acknowledgement of this work. INVESTIGATING THE MECHANISMS OF ACTION OF THE SNF2-HOMOLOG PROTEIN FUN30 Salma Awad Mahmoud A thesis submitted for the degree of Doctor of Philosophy Supervisor: Prof. Tom Owen-Hughes University of Dundee January 2011 TABLE OF CONTENTS TABLE OF CONTENTS ................................................................................... 1 LIST OF FIGURES ............................................................................................ 4 LIST OF TABLES ............................................................................................... 5 LIST OF ABBREVIATIONS ............................................................................ 6 ACKNOWLEDGMENTS .................................................................................. 7 Abstract ........................................................................................................... 9 ChI. Introduction ...........................................................................................10 1.Chromatin structure ..................................................................................10 1.1.Nucleosome ...........................................................................................10 1.1.1.DNA-histone interaction .....................................................................11 1.1.2.Nucleosome positioning......................................................................12 1.1.3.Chromatin dynamics ...........................................................................13 1.2. Higher ordered chromatin organization .................................................14 1.3. Strategies for regulating chromatin structure .........................................16 1.3.1. Histone modifications ........................................................................16 1.3.1.1. Acetylation .....................................................................................18 1.3.1.2. Histone Phosphorylation .................................................................20 1.3.1.3. Methylation and chromatin regulation .............................................21 1.3.1.4. Ubiquitination .................................................................................22 1.3.1.5. Other modifications ........................................................................24 1.3.2. Histone variants .................................................................................24 1.3.3. Nucleosome binding proteins – linker histones and HMG proteins .....26 1.3.4. Histone Chaperones ...........................................................................27 1.3.5. ATP dependent chromatin remodelling enzymes................................28 1.3.5.1. The snf2 subfamily of chromatin remodelling enzymes ...................31 1.3.5.2. Chd1 chromatin remodelling subfamily ..........................................33 1.3.5.3. ISWI chromatin organizers .............................................................34 1.3.5.4. Histone exchangers; SWR1 subfamily ............................................35 1.3.5.4.1. Swr1 ............................................................................................37 1.3.5.4.3. EP400 ..........................................................................................42 1.3.5.4.4. Etl1 ..............................................................................................44 1.3.5.4.5. Fun30 ..........................................................................................46 1.4. Roles for chromatin in genetic processes ..............................................46 1.4.1. Chromatin structure and Transcription ...............................................46 1.4.2. DNA replication and chromatin .........................................................47 1.4.3. DNA damage and repair mechanisms ................................................49 1.4.3.1. Chromatin alterations and DNA repair ............................................51 1.4.3.2. Cell cycle regulation and DNA damage ..........................................52 1.5. Aims and objectives..............................................................................54 Ch. II. Materials and Methods ......................................................................56 2.1. Purification and characterization of SWI/SNF, RSC and Fun30 ............56 2.2. Expression and purification of recombinant His-tagged Fun30 .............60 2.3. Octamer, tetramer and dimer assembly and purification ........................60 2.4. Generation of fluorescently labeled dimers ...........................................61 2.5. Preparative PCR ...................................................................................62 2.6. Purification of PCR products by ion exchange chromatography ............63 1 2.7. Chromatin assembly .............................................................................64 2.8. Immobilized template binding assay .....................................................64 2.9. Quantitative electrophoretic mobility shift assay ...................................65 2.10. ATPase assays ....................................................................................65 2.11. Glycerol velocity gradient ...................................................................66 2.12. SalI accessibility assay ........................................................................66 2.13. Nucleosome repositioning/dimer exchange assay ................................67 2.14. Western transfer of Native gels ...........................................................67 2.15. Yeast strains .......................................................................................67 2.16. Protein extraction ................................................................................68 2.17. Western Blotting .................................................................................69 2.18. Screening for drug sensitivity and sensitivity to irradiation .................70 2.19. Flow cytometry for cell cycle analysis ................................................71 2.20. Degron construction............................................................................72 2.21. Chromatin Immunoprecipitation (ChIP) ..............................................77 Ch.III: The Snf2 homolog Fun30 acts as a homodimeric ATP-dependent chromatin-remodelling enzyme ......................................................................81 3.1. Introduction ..........................................................................................81 3.2. Results ..................................................................................................83 3.2.1. Purification and characterization of the Fun30 protein complex .........83 3.2.2. Fun30 is an ATP-dependant chromatin remodelling protein ...............87 3.2.3. Fun30 binds to DNA, mononucleosomes, and nucleosome arrays ......89 3.2.4. Fun30 has ATP-dependent chromatin remodelling activity ................92 3.2.5. Fun30 can slide nucleosomes in cis and exchange H2A-H2B dimer in an ATP dependent fashion ...........................................................................94 3.2.6. Fun30 can catalyze the transfer histone octamers in trans ..................97 3.2.7. Fun30 does not exhibit specificity for ubiquitinylated HeLa histones .99 3.2.8. Fun30 has low specificity towards H2AZ......................................... 102 3.3. Discussion .......................................................................................... 105 3.4. Conclusions and perspectives ............................................................. 109 Ch. IV: FUN30 deletion results in cell cycle arrest at the G1-S transition
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