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Genetic and Molecular Characterization of Chromosome Three Heterochromatin in Drosophila Melanogaster

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Genetic and Molecular Characterization of Chromosome Three Heterochromatin in Drosophila Melanogaster Genetic and molecular characterization of chromosome three heterochromatin in Drosophila melanogaster Kathleen Anne Fitzpatrick BSc., University of British Columbia, 1980 M.Sc., University of British Columbia, 1985 THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in the Department of Molecular Biology and Biochemistry O Kathleen Anne Fitzpatrick 2005 SIMON FRASER UNIVERSITY Summer 2005 All rights reserved. This work may not be reproduced in whole or in part, by photocopy or other means without permission of the author. Approval Name: Kathleen Anne Fitzpatrick Degree: Doctor of Philosophy Title of Thesis: Genetic and molecular characterization of chromosome three heterochromatin in Drosophila melanogaster. Examininq Committee Chair: Dr. G. Tibbits, Professor Dr. B.M. Honda, Professor, Senior Supervisor Department of Molecular Biology and Biochemistry, S.F.U. Dr. D.A.R. Sinclair, Lecturer, Supervisor Department of Molecular Biology and Biochemistry, S.F.U Dr. N. Harden, Associate Professor, Supervisor Department of Molecular Biology and Biochemistry, S.F.U. Dr. D. Baillie, Professor, Internal Examiner Department of Molecular Biology and Biochemistry, S.F.U. Dr. Ross Hodgetts, Professor, External Examiner Department of Biological Sciences, University of Alberta Date Approved: April 29. 2005 ii SIMON FRASER UNIVERSITY PARTIAL COPYRIGHT LICENCE The author, whose copyright is declared on the title page of this work, has granted to Simon Fraser University the right to lend this thesis, project or extended essay to users of the Simon Fraser University Library, and to make partial or single copies only for such users or in response to a request from the library of any other university, or other educational institution, on its own behalf or for one of its users. The author has further granted permission to Simon Fraser University to keep or make a digital copy for use in its circulating collection. The author has further agreed that permission for multiple copying of this work for scholarly purposes may be granted by either the author or the Dean of Graduate Studies. It is understood that copying or publication of this work for financial gain shall not be allowed without the author's written permission. \ Permission for public performance, or limited permission for private scholarly use, of any multimedia materials forming part of this work, may have been granted by the author. This information may be found on the separately catalogued multimedia material and in the signed Partial Copyright Licence. The original Partial Copyright Licence attesting to these terms, and signed by this author, may be found in the original bound copy of this work, retained in the Simon Fraser University Archive. W. A. C. Bennett Library Simon Fraser University Bumaby, BC, Canada Abstract Heterochromatin comprises approximately one third of the genome of the fruit fly, Drosophila melanogaster. It performs vital functions in chromosome segregation and cell division. One of the most interesting and unusual features of heterochromatin is its ability to silence genes artificially relocated near it, so the presence of active genes there is paradoxical. The presence of moderately and highly repeated sequences within heterochromatin and the absence of such features as meiotic recombination and polytene banding, make it difficult to study using standard genetic approaches. For example, although heterochromatin comprises approximately 60Mb of DNA, the earliest releases of the genome project included almost no heterochromatic sequence. More recent releases provide only about 21 Mb of sequence on a series of non-contiguous scaffolds, the majority of which remain unlocalized. My work has focused on two relatively poorly characterized heterochromatic regions: the right arm of chromosome 3 (3R) and a distal portion of 3L heterochromatin (distal h47). A large number of genetic mutations have been made via P-element insertion, excision and male recombination, and by X-ray mutagenesis. These mutations provide useful new tools for the identification and characterization of genes in these regions. In particular the deficiencies will allow a means for mapping computer generated gene models by PCR. The genetic and molecular tools developed for work with these previously unexplored regions will help advance our understanding of the organization and function of sequences in heterochromatin. They also provide a necessary foundation for a complete functional annotation of genes within these unusual and poorly understood regions of the chromosome. iii Acknowledgements I wish to thank my supervisor, Dr. Barry Honda, for providing me with the opportunity to work in this fascinating field, and for providing support and assistance throughout the project, especially as it drew to a close. I am also grateful to Drs. Nick Harden and Mike Smith, both members of my original committee, who sat through many meetings, providing encouragement and support throughout. Members of the Honda lab, in particular Monika Syrzycka and Sandra Schulze, have been enormously helpful, both scientifically and with coffee and emotional support. Dr. Vett Lloyd has been an inexhaustible source of support, ideas, suggestions, and has provided valuable feedback and encouragement throughout this very busy year. Dr. Don Sinclair, also a committee member, deserves special mention. He has been a bottomless well of information, encouragement, ideas, resources and nachos, for which I am eternally grateful. One aspect of working in science is the opportunity to interact with other scientists. The following people generously provided strains and information: Dr. Alexei Tulin at the Carnegie Institute for some strains and talk about Parp; Dr. R. Levis, for P-element lines in chromosome 3 heterochromatin that he balanced before sending me; Dr. M. Leptin and Dr. lrion who shared alleles from their abstraMscreen; and Dr. A. Bejsovec who sent an allele of zeppelin. Also Dr. James Ehrman, who prepared the scanning EM images in chapter 4 and Alistair Coulthard, who examined some of the newly induced deficiencies cytologically. Finally I want to thank my son, Christopher Devine, and husband, Bill Devine, who were supportive and helpful throughout. Table of Contents .. Approval ...........................................................................................................................................11 ... Abstract ........................................................................................................................................... 111 Acknowledgements ....................................................................................................................... iv Table of Contents ............................................................................................................................ v ... List of Tables ................................................................................................................................VUI List of Figures ..................................................................................................................................x ... List of Abbreviations & Definitions ..........................................................................................xlll CHAPTER ONE: GENERAL INTRODUCTION.......................................................... I What is heterochromatin? ............................................................................................................. 2 Cytological appearance ...............................................................................................................................2 Molecular organization ...............................................................................................................................3 Chromatin structure .....................................................................................................................................4 Non-genic hnctions of heterochromatin .................................................................................................5 Centromeric functions ............................................................................................................................6 Position-effect variegation ..........................................................................................................................8 Heterochromatin proteins ..........................................................................................................................10 Heterochromatin in Drosophila melanogaster .........................................................................................13 Heterochromatic Genes in Drosophila .................................................................................... 17 Identification of essential loci in heterochromatin ..................................................................................17 Characteristics of heterochromatic genes in Drosophila .......................................................................23 Heterochromatic genes require heterochromatic proteins to function .................................................. 27 Heterochromatic genes on chromosome 3 ...............................................................................................28 Why study heterochromatin? ....................................................................................................................33 Project aims ................................................................................................................................................34
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