Cis-Regulatory divergence and expression of ryanodine receptor paralogues in Medaka (Oryzias latipes)

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Cis-Regulatory divergence and expression of ryanodine receptor paralogues in Medaka (Oryzias latipes)
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    Cis  -Regulatory divergence and expression of ryanodine receptor paralogues in Medaka ( Oryzias latipes  ) Tahani Baakdhah Supervisor: Dr. Jens Franck A Thesis Submitted to the Faculty of Graduate Studies in Partial Fulfilment of the Requirements for the Masters of Science Degree. Department of Biology Masters of Science in BioScience, Technology and Public Policy Program The University of Winnipeg Winnipeg, Manitoba, Canada December 2011 Copyright 2011 © Tahani Baakdhah  A BSTRACT Ryanodine receptors (RyRs) are large homotetrameric proteins that in mammals are encoded by three genes: RyR1 in skeletal muscle; RyR2 in cardiac and smooth muscle; and RyR3 which is expressed in a diversity of cell types. RyR channels play a central role in the excitation-contraction (EC) coupling process by mediating Ca² +  release from the sarcoplasmic reticulum (SR). RyR1 paralogues are expressed in a fiber type-specific manner in fish skeletal muscles: RyR1a in slow-twitch skeletal muscle (red muscle) and RyR1b in fast-twitch skeletal muscle (white muscle). RyR1a and RyR1b are classic examples of spatial subfunctionalization, since they share an ancestral function, yet are expressed differentially in red and white muscle fibres respectively.   Gene duplication and subsequent divergence in sequence, expression and interactions are considered to be one of the major driving forces in the evolution of diversity. After the upstream promoter regions, evolutionarily conserved introns are considered the second most important sites containing gene regulatory elements that control tissue-specific expression (gene enhancers or gene silencers). Using medaka ( Oryzias latipes ) as a model organism, I searched the noncoding sequences in medaka RyR1 and RyR3 genes to look for conserved noncoding elements for RyR co-orthologues and paralogues. The bioinformatic analyses revealed evidence of conservation of noncoding elements for RyR co-orthologues and divergence between RyR  paralogues. I also analyzed the spatial and developmental expression of the RyR paralogues (RyR1a/RyR1b; RyR3a/RyR3b) in medaka. The expression analyses revealed conserved expression patterns for the RyR co-orthologues and divergent expression of the RyR paralogues.   ii  A CKNOWLEDGMENTS  I would never have been able to finish my dissertation without the guidance of my committee members, help from friends, and support from my husband and my family. First and foremost I offer my sincerest gratitude to my supervisor, Dr. Jens Franck, for his continued guidance, caring, patience, and effort to provide me with an excellent atmosphere for research. I attribute a great part of my Master’s degree to his unshakeble support and without him this thesis would not have been completed. One simply could not wish for a better and friendlier supervisor. I would also like to warmly thank Dr. Good for her critical guidance and   input throughout the process of this research, as well as Dr. Civetta who was always willing to help and give his best scientific advice and suggestions. I would also like to acknowledge Robyn Cole for her great work in the animal complex, especially the fish aquarium, where she was taking care of fish feeding and  breeding as well as being a great help to me in handling the fish throughout the process of this research. In my daily work I have been blessed with a friendly and cheerful group of fellow students. Many thanks to Fatimah Alsaffar for helping me in collecting tissues samples, feeding the fish and collecting medaka eggs. I am also indebted to my many colleagues who supported me including: Saivash Darbandi, Ian Kasloff, Rebecca Vanderhooft, Nada Sagga, and Maram Felemban. iii  I dedicate this dissertation to my husband, Wael Alnami. He always stood by me through the good and bad times. Thank you dear Wael, you made my dream come true. My kids Hashim Alnami and Ahmad Alnami were my inspiration; they filled my life with joy and happiness necessary to reach my goals. I would also like to thank my parents, my father Waheeb Baakdhah, my mother Amal Abualjadayl, They were always encouraging me with their wishes and prayers. Special thanks for the Saudi Arabian Cultural bureau for giving me this opportunity and for supporting my research. Last but not least, my family and friends back home and the one above all of us, God, for answering my prayers and giving me the strength to plod on despite my constitution wanting to give up, thank you so much Allah for making all things possible.   Iv  T ABLE OF C ONTENTS v 1.2.1 Overview ………………………………………………………….. .. … . . ......10 1.1.4 RyR role in disease……… . ……………………... ............................ ... ............8 1.1.3   RyR Expression ……………… . ……………………………….. ......... ..... .......6 1.1.2   Role in excitation contraction coupling…………………… .. ….. ..... ..... … .....4 1.1.1   Structure………………………………………………….……….. ........ ... .....2 1.1   Ryanodine Receptors (RyRs) …………………………………… ... …… . ... …. .. .....2 Chapter 1: Liter  ature Review…………………………………………………… . . … ........1 Abbreviations and Nomenclatures.......................................................... ................ ........xvi List of Appendices............................................................................. ..................... .........xiv List of Figures.......................................................................................... ...................... ...xi List of Tables...................................................... ................... ................................ ... .........x   Acknowledgements.......................................................................... .................. ... . ..........iii Abstract......................................................................................... .... ...... .................. ........ii 1.2 Evolution of duplicated genes …………………………………… . …… .......... … .10 1.2.2 Evolutionary fate of duplicate genes …………………………… .... ....... . . ......13 1.2.3 Contributions of gene duplication to genomic and organismal evolution ........ 14 
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