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Genomic Imprinting and X Chromosome Dosage Compensation in Domestic Ruminants Jingyue Duan [email protected]

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Genomic Imprinting and X Chromosome Dosage Compensation in Domestic Ruminants Jingyue Duan Jingyue.Duan@Uconn.Edu University of Connecticut OpenCommons@UConn Doctoral Dissertations University of Connecticut Graduate School 11-30-2018 Genomic Imprinting and X Chromosome Dosage Compensation in Domestic Ruminants Jingyue Duan [email protected] Follow this and additional works at: https://opencommons.uconn.edu/dissertations Recommended Citation Duan, Jingyue, "Genomic Imprinting and X Chromosome Dosage Compensation in Domestic Ruminants" (2018). Doctoral Dissertations. 2015. https://opencommons.uconn.edu/dissertations/2015 Genomic Imprinting and X Chromosome Dosage Compensation in Domestic Ruminants Jingyue (Ellie) Duan, Ph.D. University of Connecticut, 2018 Abstract In diploid cells, genes are presumed to be expressed from both alleles to maintain gene dosage for normal development. However, a small number of genes reach haplosufficiency even with only one functional allele per cell. Most of these genes are regulated through genomic imprinting and X chromosome inactivation (XCI). DNA methylation is an essential epigenetic regulation for developmental programming in embryogenesis and play crucial roles in genomic imprinting and XCI. This dissertation presents 1) effects of maternal diets on genome imprinting in fetal sheep (Chapter Two), 2) dosage compensation of the X chromosomes in bovine germline, embryos and somatic tissues (Chapter Three), 3) Whole genome DNA methylation in bovine in vivo preimplantation development (Chapter Four). In chapter two, we report the first throughput study of genomic imprinting in sheep and report the identification of 13 new imprinted genes as well as demonstrating that maternal diets affect expression of imprinted genes in fetuses. Our results determine maternal diets influence imprinted gene expression while the parental-of-origin expression pattern was not affected, further suggesting that gene expression levels and imprinted patterns may be regulated through different epigenetic mechanisms. In chapter three, we reported the up-regulation of X chromosome in bovine germline, embryos and somatic tissues, supporting a balanced expression between a single active X and autosome pairs. However, deviating from Ohno’s theory, dosage compensation to rescue X haploinsufficiency appears to be an incomplete process for expressed genes but a complete process for “dosage-sensitive” genes. In chapter four, we adopted the scWGBS-seq method to comprehensive profile 5-MeC in single-cytosine Jingyue (Ellie) Duan – University of Connecticut, 2018 resolution in bovine sperm, immature oocyte, in vivo/vitro mature single oocyte, and in vivo developed 2-, 4-, 8-, 16-cell single embryos. We observed global demethylation during bovine embryo cleavage up to 8-cell stage and de novo methylation at 16-cell stage. Our results refined the current knowledge on bovine embryo DNA methylation dynamics and provide valuable resources for future studies. Title Page Genomic Imprinting and X Chromosome Dosage Compensation in Domestic Ruminants Jingyue (Ellie) Duan B.S., Sichuan University, P.R. China, 2014 M.S., University of Connecticut, U.S.A, 2017 A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy at the University of Connecticut 2018 Copyright by Jingyue (Ellie) Duan 2018 ii Approval Page Doctor of Philosophy Dissertation Genomic Imprinting and X Chromosome Dosage Compensation in Domestic Ruminants Presented by Jingyue (Ellie) Duan, B.S., M.S. Major Advisor __________________________________________________ Dr. Xiuchun (Cindy) Tian Associate Advisor__________________________________________________ Dr. Ion Mandoiu Associate Advisor__________________________________________________ Dr. Lynn Kuo Associate Advisor__________________________________________________ Dr. Michael O’Neill University of Connecticut 2018 iii DEDICATION This dissertation is dedicated to my first biology teachers in the middle school, late Mr. Liewen Yang, who asked me what is cloning. iv ACKNOWLEDGMENTS I would like to express my deepest gratitude to my major advisor Dr. Xiuchun (Cindy) Tian for your instruction, encourage and support. Thank you for believe in me and motivate me to overcome challenges over the past four years. Your patient guidance helps me become a skilled and independent scientist. You are not only an advisor of my research but also a mentor of my life. Through you, I see the life of a creative, ingenuity, intelligent female scientist, and I see an independent, strong, caring, supportive mother. You are a person inspired me the most in my life, what I have learned from you are invaluable. Thank you. I would like to thank my committee members Dr. Ion Mandoiu, Dr. Lynn Kuo, and Dr. Michael O’Neill, for your help, support and insight. Thank you for your instruction in data analysis, statistical analysis and biological knowledge. Thank you for your valuable feedback and comments that made my dissertation thesis possible. I would like to thank all my collaborators in my projects, for your help in making these projects possible. Dr. Nathaniel Jue, Dr. Rachel O’Neill, Wei Shi, Dr. Sahar Seesi, Fahad AlQahtani, Dr. Sadie Marjani, Dr. Isabelle Hue, Dr. Amanda Jones, Dr. Sambhu Pillai, Dr. Maria Hoffman, Dr. Sarah A Reed, Dr. Kristen Govoni, Dr. Steve Zinn. Thank you for your help and expert advice in statistical analysis, computational approaches, experimental design and providing the valuable samples used in the experiment. I would like to thank the Animal science department main office, graduate students, and faculty for your kindness and support. To my current and previous fellow graduate students, post-doc and visiting scholars, Lang Sun, Liqi An, Dr. Zongliang Jiang, Linkai Zhu, Kaleigh Flock, Ling Wang, Dr. Kanokwan Srirattana, Elizabeth Johnson, Shyann Williams, Lindsay Bavone, Taiye Adakole, Dr. Rashid Ali, Dr. Chuanjie Zhang, Chang Huang, Jacob Ricker, Cabrera Juan, Qian Du, Dr. Delun Huang, Dr. v Mingyuan Zhang, Dr. Limin Wang, Dr. Huan Yang, Dr. Junhe Hu, and Dr. Junli Zhu. Thank you for sharing your expertise with me in the lab, and for your support, help and friendship in my life. A special thanks to Dr. Zongliang Jiang, Kaleigh Flock, Dr. Mingyuan Zhang, Elizabeth Johnson for your collaboration and lab experiment expertise in two projects present in my dissertation, without your help, I couldn’t achieve this much. I would like to thank my previous advisor Dr. Qun Sun, Life Science College vice dean Dr. Yun Zhao in Sichuan University (SCU) and CAHNR dean Dr. Cameron Faustman. Thank you for initiating the 3+1 exchange program between SCU and UCONN. I would like to thank Dr. Robert Milvae, Dr. Kumar Venkitanarayanan, Dr. Hedley Freake for recruiting me in this exchange program. This was a life-changing experience in my undergrad senior year. I got more opportunities to learn and to see the world. Lastly, I would also like to thank my family and friends for your love and support. Shanglong, thank you for loving me, taking care of me, understanding me, and supporting me through every challenge. Mom and Dad, thank you for always encouraging me to pursue my dream and believing in me. Dear friends, Suiyuan, Qianyue, Ruixuan, Manqian, and Xiaogang, thank you for being my friends. I have been friends with some of you since primary school, it means so much to me that we support each other achieve our goals and follow our dreams. Thank you for being there for me through this journey. vi Table of contents Abstract ............................................................................................................................................ i Title Page ......................................................................................................................................... i Approval Page ................................................................................................................................ iii DEDICATION ............................................................................................................................... iv ACKNOWLEDGMENTS .............................................................................................................. v Table of contents ........................................................................................................................... vii List of Common Abbreviations ...................................................................................................... x List of Tables and Figures.............................................................................................................. xi List of Tables ............................................................................................................................. xi List of Figures ........................................................................................................................... xii List of Supplementary Tables .................................................................................................. xiii List of Supplementary Figures .................................................................................................. xv Chapter One .................................................................................................................................... 1 Introduction ..................................................................................................................................... 1 1.1. Epigenetics ..........................................................................................................................
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