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Gene Conversions in the Siglec and CEA Immunoglobulin Gene Families

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Gene Conversions in the Siglec and CEA Immunoglobulin Gene Families Gene conversions in the Siglec and CEA immunoglobulin gene families of primates Mouldi Zid Thesis submitted to the Faculty of Graduate and Postdoctoral Studies of the University of Ottawa in partial fulfillment of the requirements for the M.Sc. degree in the Ottawa Carlton Institute of Biology Thèse soumise à la Faculté des études supérieurs et postdoctorales de l’Université d’Ottawa en vue de l’obtention de la maîtrise en biologie de l’Institut pour la biologie Ottawa Carlton © Mouldi Zid, Ottawa, Canada, 2013 1 Examiners The following members of the Ottawa Carlton Institute of Biology Dr. Guy Drouin Supervisor Dr. Michel Dumontier Examining Member (Carleton University) Dr. Stéphane Aris-Brosou Examining Member (University of Ottawa) Dr. Marcel Turcotte Examining Member (University of Ottawa) 2 Table of contents Acknowledgements .................................................................................................................... 5 List of tables ............................................................................................................................... 6 List of figures .............................................................................................................................. 7 List of abbreviations ................................................................................................................... 8 Abstract ...................................................................................................................................... 9 Résumé .................................................................................................................................... 10 Chapter 1. Introduction ............................................................................................................. 11 1. Gene conversions ................................................................................................................. 11 1.1. Mechanism of gene conversion ..................................................................................... 11 1.3. Methods for detecting gene conversion ........................................................................ 16 2. Immunoglobulin superfamily ................................................................................................. 16 2.1. Siglec family ................................................................................................................... 18 2.2. CEA family ...................................................................................................................... 25 3. Objectives .............................................................................................................................. 30 Literature cited ........................................................................................................................... 31 Chapter 2. Gene conversions are frequent but not under positive selection in the Siglec gene families of primates .................................................................................................................. 45 Abstract ..................................................................................................................................... 45 2.1. Introduction ......................................................................................................................... 46 2.2. Materials and methods ....................................................................................................... 49 2.3. Results ............................................................................................................................... 52 2.3.1. Number, lengths and polarity of gene conversions .................................................... 52 2.3.2. Sequence similarities and GC-content of converted and non-converted regions ..... 53 2.3.3. Biased distribution of converted regions .................................................................... 53 2.3.4. Tests of selection ........................................................................................................ 54 2.4. Discussion .......................................................................................................................... 56 Acknowledgements ................................................................................................................... 62 Literature cited ........................................................................................................................... 63 Figure legends ........................................................................................................................... 69 Supplemental Table 2.1 ............................................................................................................ 74 Supplemental Table 2.2 ............................................................................................................ 76 Chapter 3. Gene conversions are under purifying selection in the carcinoembryonic antigen immunoglobulin gene families of primates ................................................................................ 77 Abstract ..................................................................................................................................... 77 3.1. Introduction ......................................................................................................................... 78 3.2. Materials and methods ....................................................................................................... 81 3.3. Results ............................................................................................................................... 84 3.3.1. Number, lengths and direction of gene conversion .................................................... 84 3.3.2. Sequence similarities and GC-content of converted and non-converted regions ..... 86 3.3.3. Biased distribution of converted regions .................................................................... 86 3.3.4. Tests of selection ........................................................................................................ 87 Discussion ................................................................................................................................. 89 Acknowledgements ................................................................................................................... 92 Literature cited ........................................................................................................................... 94 3 Figure legends ......................................................................................................................... 102 Supplemental Table 3.1 .......................................................................................................... 109 Supplemental Table 3.2 .......................................................................................................... 111 Chapter 4. General conclusions ............................................................................................. 112 Literature cited ......................................................................................................................... 115 4 Acknowledgements I would like to thank my supervisor, Dr. Guy Drouin, for the opportunity that he gave me to do this MSc. degree at the University of Ottawa. His cheerful guiding throughout my program was an extraordinary experience and gift for me. As well as, I would sincerely like to thank him for reviewing my thesis. I would also like to thank Dr. Stéphane Aris-Brosou who provided me with valuable advice and guidelines. In addition, I would like to thank you Dr. Marcel Turcotte and Dr. Michel Dumontier for agreeing to be a members of my graduate committee. Finally, I would like to thank all of my fellow graduate students that helped me in various ways throughout my MSc. degree. 5 List of tables Table 2.1 Gene conversions, and their location, in the CD33rSiglec genes of five primate species………………………………………….………………………………………………...…68 Table 2.2 dN and dS values for Ig-like V-type1 and Ig-like C2-type 1 domains……............69 Table 3.1 Gene conversions, and their location, in the CEA genes of five primate species…………………………………………..…………………………...…………….……...101 Table 3.2 dN/dS ratios ( ω) of Ig-like V-type 1 and Ig-like C2-type 1 domains…………………………………………..……………………..…….………..……….102 6 List of figures Figure 1.1 Mechanisms of gene conversion …………………………..………..……………..13 Figure 1.2 Structure of human Siglecs genes……………………………….……….…..........20 Figure 1.3 Expression pattern of human Siglecs in immune cells.…………………..........…24 Figure 1.4 Organisation and tissue expression of the human CEACAM genes….………...27 Figure 1.5 Organisation of the human PSG genes…..…………………..………….…..........28 Figure 2.1 Structure and tissue expression of Hominid Siglecs…..………….…….…..........71 Figure 2.2 Organisation of CD33rSiglec genes and gene conversions in five primate species…..……………………………………………………………………………………….....72 Figure 2.3 Phylogenetic tree of human Siglecs proteins…………..………….…….……......73 Figure 2.4 Schematic representation of the structure of CD33rSiglec proteins and location of the gene conversions detected between the CD33rSiglec genes of five primate species……………………………………………......………………...……………………..……74 Figure 3.1 Structure and tissue expression of human CEACAM proteins..………...……..105 Figure 3.2 Structure of human PSG proteins………………......………………...……...…...106
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