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Trna GENES AFFECT MULTIPLE ASPECTS of LOCAL CHROMOSOME BEHAVIOR

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Trna GENES AFFECT MULTIPLE ASPECTS of LOCAL CHROMOSOME BEHAVIOR tRNA GENES AFFECT MULTIPLE ASPECTS OF LOCAL CHROMOSOME BEHAVIOR by Matthew J Pratt-Hyatt A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Cellular and Molecular Biology) in The University of Michigan 2008 Doctoral Committee: Professor David R. Engelke, Chair Professor Robert S. Fuller Associate Professor Mats E. Ljungman Associate Professor Thomas E. Wilson Assistant Professor Daniel A. Bochar © Matthew J. Pratt-Hyatt All rights reserved 2008 . To my loving family Who’ve helped me so much ii Acknowledgements I would first like to thank my mentor, David Engelke. His help has been imperative to the development of my scientific reasoning, writing, and public speaking. He has been incredibly supportive at each phase of my graduate career here at the University of Michigan. Second, I would like to thank the past and present members of the Engelke lab. I would especially like to thank Paul Good, May Tsoi, Glenn Wozniak, Kevin Kapadia, and Becky Haeusler for all of their help. For this dissertation I would like to thank the following people for their assistance. For Chapter II, I would like to thank Kevin Kapadia and Paul Good for technical assistance. I would also like to thank David Engelke and Tom Wilson for help with critical thinking and writing. For Chapter III, I would like to thank David Engelke and Rebecca Haeusler for their major writing contribution. I would also like to acknowledge that Rebecca Haeusler did the majority of the work that led to figures 1-3 in that chapter. For Chapter IV, I would like to thank Anita Hopper, David Engelke and Rebecca Haeusler for their writing contributions. I would also like to acknowledge Rebecca Haeusler’s work that led to figure 4.2 in that chapter. I would also like to thank my parents, Peggy and John Hyatt, for their encouragement and support. They instilled in me the importance of intellectual investigation.. Finally, I wish to thank my wife, Jennifer, and my daughter, Genevieve, who make my life fun and exciting. Jen is such a supportive person and I don’t know where I would be without her. She is always there to help me see the big picture. iii Table of Contents Dedication.......................................................................................................................ii Acknowledgements ........................................................................................................iii List of Figures ................................................................................................................vi List of Tables ................................................................................................................vii List of Abbreviations....................................................................................................viii Abstract..........................................................................................................................ix Chapter I. Introduction............................................................................................1 tRNA genes and Homologous Recombination..........................................1 tRNA genes are localized to the nucleolus................................................2 Silencing of pol II transcription in Saccharomyces cerevisiae ..................3 Silencing near tRNA genes.......................................................................3 Mod5p, a tRNA modifying enzyme..........................................................5 II. Increased recombination between tRNA genes...................................10 Abstract ...............................................................................................10 Introduction............................................................................................11 Materials and Methods ...........................................................................12 Recombination between identical tRNA genes .......................................13 Recombination Path ...............................................................................15 Recombination between retrotransposon LTR elements..........................16 Discussion..............................................................................................16 Acknowledgements ................................................................................18 III. Clustering of yeast tRNA genes is mediated by specific association of Condensin with tRNA gene transcription complex.............................23 Abstract..................................................................................................23 Introduction............................................................................................24 tRNA genes remain clustered at the nucleolus throughout the cell cycle.......................................................................................................26 Nucleolar localization of tRNA gene clusters require microtubules.........27 Clustering of tRNA genes is condensin-dependent .................................28 Condensin is bound preferentially to tRNA genes...................................30 Discussion..............................................................................................31 Materials and Methods ...........................................................................35 Acknowledgements ................................................................................38 iv IV. Mod5p, a tRNA modifying enzyme, binds to tRNA gene complexes and affects local transcriptional silencing ...........................................45 Abstract..................................................................................................45 Introduction............................................................................................46 Materials and Methods ...........................................................................47 Mod5p is required for silencing near tRNA genes...................................51 Mod5p and Maf1p are not involved in the subnuclear distribution of the tRNA genes ......................................................................................52 mod5∆ does not alleviate repression of tRNA gene transcripts................53 Role of Mod5p catalytic activity in tgm silencing...................................53 The effects of Mod5 mutation on tgm silencing......................................54 Mod5p homologs restore tgm silencing ..................................................55 Mod5p is present at tRNA genes ............................................................56 Mod5p associates with RNA polymerase III transcription complex components ............................................................................................57 Discussion..............................................................................................58 Acknowledgements ................................................................................61 V. Conclusion ............................................................................................72 tRNA transcription and recombination ...................................................72 tRNA gene nucleolar localization ...........................................................74 Mod5p is necessary for tgm silencing.....................................................75 Appendix.......................................................................................................................78 Bibliography .................................................................................................................86 v List of Figures Figure 1.1 Three subcomplexes bind in subsequent order that leads to tRNA gene transcription.........................................................................................................8 1.2 Mod5p catalyzes the addition of an isopentenyl group from DMAPP onto position 37 of the tRNA.......................................................................................9 2.1 Recombination between tRNA genes .................................................................21 2.2 Recombination between Ty3 sigma direct repeats ..............................................22 3.1 In situ hybridization of unsynchronized and nocodazole treated cells .................40 3.2 Condensin mutants release tgm silencing ...........................................................41 3.3 Condensin mutants show loss of tRNA gene and pre-tRNA nucleolar localization ........................................................................................................42 3.4 Condensin subunits Smc2 and Smc4 interact with tRNA genes..........................43 3.5 Condensin subunits Smc2 and Smc4 interact with subunits of RNA polymerase III and its transcription factors.........................................................44 4.1 Deletion of MOD5 releases tgm silencing ..........................................................63 4.2 mod5∆ and maf1∆ do not cause mislocalization of tRNA genes .........................64 4.3 mod5∆ does not alleviate repression of pol III genes mediated by Maf1p...........43 4.4 DMAPP depletion does not affect tgm silencing ................................................66 4.5 Alignment of homologs of Mod5p .....................................................................67 4.6 Mod5p mutants..................................................................................................68 4.7 Silencing functions of Mod5p are
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