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Identification and Characterization of Rearrangements in the Vervet Monkey Genome

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Identification and Characterization of Rearrangements in the Vervet Monkey Genome Identification and characterization of rearrangements in the vervet monkey genome by AmanPreet Badhwar Department of Ruman Genetics McGill University, Montreal August 2006 A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Master of Science Copyright © AmanPreet Badhwar, 2006 1 Library and Bibliothèque et 1+1 Archives Canada Archives Canada Published Heritage Direction du Branch Patrimoine de l'édition 395 Wellington Street 395, rue Wellington Ottawa ON K1A ON4 Ottawa ON K1A ON4 Canada Canada Your file Votre référence ISBN: 978-0-494-32815-6 Our file Notre référence ISBN: 978-0-494-32815-6 NOTICE: AVIS: The author has granted a non­ L'auteur a accordé une licence non exclusive exclusive license allowing Library permettant à la Bibliothèque et Archives and Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par télécommunication ou par l'Internet, prêter, telecommunication or on the Internet, distribuer et vendre des thèses partout dans loan, distribute and sell th es es le monde, à des fins commerciales ou autres, worldwide, for commercial or non­ sur support microforme, papier, électronique commercial purposes, in microform, et/ou autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriété du droit d'auteur ownership and moral rights in et des droits moraux qui protège cette thèse. this thesis. Neither the thesis Ni la thèse ni des extraits substantiels de nor substantial extracts from it celle-ci ne doivent être imprimés ou autrement may be printed or otherwise reproduits sans son autorisation. reproduced without the author's permission. ln compliance with the Canadian Conformément à la loi canadienne Privacy Act some supporting sur la protection de la vie privée, forms may have been removed quelques formulaires secondaires from this thesis. ont été enlevés de cette thèse. While these forms may be included Bien que ces formulaires in the document page count, aient inclus dans la pagination, their removal does not represent il n'y aura aucun contenu manquant. any loss of content from the thesis. ••• Canada Abstract Several mechanisms can lead to the reorganization of genomes during speciation, including centromere repositioning, new centromere emergence or other chromosomal rearrangements. Using a comparative karyotype approach, 1 determined that the vervet genome contains at least 12 evolutionary young centromere locations. To study the evolutionary dynamics of centromere formation, 1 identified and validated the alpha-satellite repeat as a centromere-specific marker in the vervet using comparative genomics, sequence analysis and hybridization screening. 1 developed criteria to infer the position of vervet bacterial artificial chromosome (BAC) inserts based on alpha-satellite monomer content. In a complementary approach, 1 demarcated the pericentromeric boundaries in human and identified vervet BAC clones that mapped orthologously to these regions. ln addition to centromeric analyses, 1 developed methodologies to detect other genome rearrangements, in particular vervet deletion/human insertion and vervet translocation events. The tools and approaches developed in this thesis will prove useful in cataloguing additional vervet genome rearrangements. 11 Résumé Plusieurs mécanismes sont susceptibles d'engendrer une réorganisation du génome lors d'une spéciation, comme par exemple un repositionnement de centromère, l'apparition de nouveaux centromères et autres réarrangements chromosomiques. En utilisant une méthode basée sur la comparaison des caryotypes, j'ai déterminé que le génome du Vervet (singe vert) contient un minimum de 12 positions centromériques récemment apparues au cours de l'évolution. Pour ce faire, j'ai utilisé une approche combinant des méthodes de génomique comparative, d'analyse de séquences et de criblage par hybridation, ce qui m'a permis d'identifier et de valider un motif répété alpha-satellite pouvant servir de marqueur spécifique pour les centromères. De plus, j'ai développé des critères pour déterminer la position des BAC (chromosomes artificiels de bactérie) du Vervet en fonction de leur composition en monomères alpha-satellites. En complément, j'ai défini les limites des péri-centromères humains et identifié les BAC du Vervet correspondant à ces régions. Par ailleurs, j'ai également développé des méthodes afin de détecter d'autres types de réarrangements chromosomiques, notamment les translocations chez le Vervet ainsi que les portions du génome délétées chez le Vervet ou insérées chez l'humain. Ces nouveaux outils faciliteront le catalogage des autres réarrangements génomiques chez le Vervet. III Table of Contents ABSTRACT ............................................................................................... II , , RESUME .................................................................................................. 111 T ABLE OF CONTENTS ......................................................................... IV TABLE OF FIGURES ............................................................................ VII T ABLE OF ABBREVIATIONS ........................................................... VIII ACKNOWLEDGEMENTS ..................................................................... IX CONTRIBUTIONS TO ORIGINAL KNOWLEDGE ........................ XIII CHAPTER ONE ......................................................................................... 1 INTRODUCTION ..............•....•..•.••••••.•.••••..••••••••......•.....•............................. 1 1.1 Nonhuman primates in research ...................................................................... 1 1.2 Vervet monkey as a biomedical mode!.. ........................................................... 5 1.2.1 Attractive vervet attributes for biomedical research ...................... 6 1.2.2 Availability ofvervet genetic resources ......................................... 8 1.3 Vervet monkey as a model ofgenome evolution ............................................... 9 1.4 Vervet physical map project .......................................................................... Il 1. 4.1 BA C Cloning System ................................................................... 12 1.4.2 Vervet BAC End Sequencing ....................................................... 13 1.4.3 Vervet BAC library ..................................................................... 14 1.5 Research Aims................................................... ............................................ 15 CHAPTER TW0 ...................................................................................... 17 CHROMOSOMAL EVOLUTION IN THE VERVET .......................................... 17 2.1 Preface .......................................................................................................... 17 IV 2.2 Analyses ofa humanlrhesus/vervet synteny map ............................................ 17 2.3 Identification ofconserved centromere positions ........................................... 19 2.4 Identification ofevolutionary recent centromere positions ............................ 19 2.5 Identification ofother ultra structural modifications ..................................... 20 2.6 Mechanisms oflineage-specific karyotype change in the vervet ..................... 20 2.6.1 Centromere repositioning ........................................................... 21 2.6.2 Genome rearrangements ............................................................. 24 2. 7 Summary ....................................................................................................... 25 CHAPTER THREE .................................................................................. 26 USE OF ALPHA-SATELLITE REPEAT AS A CENTROMERE MARKER .............26 3.1 Preface .......................................................................................................... 26 3.2 Human and chimpanzee analysis ofcentromere markers ............................... 28 3.3 Detection ofBACs with ALR content using sequence analysis ....................... 32 3.4 Detection ofBACs with ALR content by hybridization screening ................... 33 3.5 Reproducibility ofALR BAC detection by the two techniques ........................ 36 3.6 Presence of divergent ALR monomers in the vervet genome .......................... 37 3.7 The use ofALR organization to predict centromeric positions ....................... 39 3.8 Summary ....................................................................................................... 42 CHAPTER FOUR ..................................................................................... 43 CHROMOSOME W ALKING INTO PERICENTROMERIC REGIONS ............... 43 4.1 Preface .......................................................................................................... 43 4.2 Estimation ofhuman pericentromeric boundaries ......................................... 43 4.3 Test for cloning bias in human pericentromeric regions ................................ 45 4.4 Identification ofpericentromeric vervet BACs ............................................... 46 4. 5 Insights into old and new centromere organization in the vervet ................... 51 4.6 Summary ....................................................................................................... 54 CHAPTER
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