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Mechanistic Basis for Control of Early Embryonic Development by a 5’ Trna Fragment

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Mechanistic Basis for Control of Early Embryonic Development by a 5’ Trna Fragment University of Massachusetts Medical School eScholarship@UMMS GSBS Dissertations and Theses Graduate School of Biomedical Sciences 2019-07-08 Mechanistic Basis for Control of Early Embryonic Development by a 5’ tRNA Fragment Xin Y. Bing University of Massachusetts Medical School Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_diss Part of the Cell and Developmental Biology Commons, and the Genomics Commons Repository Citation Bing XY. (2019). Mechanistic Basis for Control of Early Embryonic Development by a 5’ tRNA Fragment. GSBS Dissertations and Theses. https://doi.org/10.13028/6bvg-x092. Retrieved from https://escholarship.umassmed.edu/gsbs_diss/1035 Creative Commons License This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Dissertations and Theses by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. Mechanistic Basis for Control of Early Embryonic Development by a 5’ tRNA Fragment A Dissertation Presented By XINYANG BING Submitted to the Faculty of the University of Massachusetts Graduate School of Biomedical Sciences, Worcester in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY th July 8 2019 Interdisciplinary Graduate Program ii MECHANISTIC BASIS FOR CONTROL OF EARLY EMBRYONIC DEVELOPMENT BY A 5’ tRNA FRAGMENT A Dissertation Presented By XINYANG BING This work was undertaken in the Graduate School of Biomedical Sciences Interdisciplinary Graduate Program Under the mentorship of Oliver Rando, M.D. Ph.D., Thesis Advisor Paul Kaufman, Ph.D., Member of Committee Sean Ryder, Ph.D., Member of Committee Pavel Ivanov, Ph.D., External Member of Committee Thomas Fazzio, Ph.D., Chair of Committee Mary Ellen Lane, PhD., Dean of the Graduate School of Biomedical Sciences July 8th 2019 iii This work is dedicated to Mom and dad Silvia And Helena, Baba will always love you. iv ACKNOWLEDGEMENTS “A teacher for one day is a father for life” – Chinese idiom. With that in mind, I would like to thank my thesis mentor Oliver Rando. Ollie has taught me so much about not only how to rigorously conduct scientific inquiry, but how to approach science, mentorship, and life in general. His keen insight, breadth of knowledge, patience, generosity, and work ethic was a constant source of inspiration. The wealth of knowledge and experience that he has so kindly shared with me, I think sometimes maybe even unwittingly, will surely guide me throughout the rest of my career. To my colleagues, thank you. It takes a village to raise a child, and without the members of the Rando lab and the UMass scientific community in general, I would certainly not have been able to complete my dissertation. From my first day in the lab, Upasna Sharma has been a patient and wonderful mentor to me. Since my project is also based on her findings, I owe much to her trailblazing. I specially thank Fengyun Sun for his guidance, expertise, and friendship; Io Long Chan, Shweta Kukreja, Nils Kriestenstein, Caroline Galan, Ebru Kaymak, Vera Rinaldi, and Colin Conine for help and discussions; past lab members Stanley Hsieh Tsung-Han, Caitlin Connelly, Ben Carone, Amanda Hughes, Jeremy Shea, Markus Vallaster for friendship and discussions. Thank you Lina Song for helping provide timely advice and support for the lab and I. Special thank you to Thomas Fazzio and his lab members Sarah Hainer, Kurtis McCannel, and Benson Chen for their help and reagent support. I am indebted to my thesis committee members Tom, Paul Kaufman and Sean Ryder for their support and discussions. v Last but not definitely not least, thank you so much Ana Bošković for being a great collaborator, superb mentor and friend. I would also like to thank our collaborators Joanna Jachowicz and Maria- Elena Torres-Padilla for giving me the opportunity to better my computational skills. Thank you to all who have provided me with guidance, advice, and know- how: Emiliano Ricci, Wu Pei-Hsuan, Michal Rabani, Ozlem Yildirim, Dante Lepore, Tania Silva, Nick Rhind lab, Marian Walhout lab, Anastasia Khvorova lab, and Phil Zamore lab. Lastly, thank you to my friends who have supported me throughout my Ph.D. and inspired me when I was lost, Ammeret Rossouw, Juliano Sangalli, Teresa Rzezniczak, and Michael Packer. And thank you to my old mentors Thomas Merritt and Brent Sinclair for giving me the opportunity to train and learn with you, and all the people I worked with in their labs. vi ABSTRACT Ancestral environmental conditions can instruct offspring development, although the mechanism(s) underlying such transgenerational epigenetic inheritance is unclear. In murine models focused on paternal dietary effects, we and others have identified tRNA fragments (tRFs) in mature sperm as potential carriers of epigenetic information. In our search for molecular targets of specific tRFs, we observed that altering the level of 5’-tRF Glycine-GCC (tRF-GG) in mouse embryonic stem cells (mESCs) and preimplantation embryos modulates the expression of the endogenous retrovirus MERV-L and genes regulated by MERV-L. Intriguingly, transient derepression of MERV-L is associated with totipotency of two-cell stage embryos and a subset of two-cell-like mESCs. Here, I reveal the mechanistic basis for tRF-GG regulation of MERV-L. I show that tRF-GG supports the production of numerous small nuclear RNAs associated with the Cajal body, in mouse and human embryonic stem cells. In particular, tRF-GG modulates the levels of U7 snRNA to ensure an adequate supply of histone proteins. This in turn safeguards heterochromatin-mediated transcriptional repression of MERV-L elements. Importantly, tRF-GG effects on histone mRNA levels, activity of a histone 3’UTR reporter, and expression of MERV-L associated transcripts can all be suppressed by appropriate manipulation of U7 RNA levels. I also show that hnRNPF and H bind directly to tRF-GG, and display a stark overlap of in vivo functions to tRF-GG. Together, this data uncovers a conserved mechanism for a 5’ tRNA fragment in the fine- vii tuning of a regulatory cascade to modulate global chromatin organization during pre-implantation development. viii TABLE OF CONTENTS Dedication ....................................................................................................... iii Acknowledgements ......................................................................................... iv Abstract ........................................................................................................... vi Table of Contents ............................................................................................ viii List of Figures.................................................................................................. x List of Copyrighted Materials Produced by the Author .................................... xii List of Third Party Copyrighted Materials ........................................................ xiii Preface ............................................................................................................ xiv CHAPTER I: Introduction ................................................................................ 1 Overview ........................................................................................................ 1 Inter- and Transgenerational Epigenetic Inheritance ..................................... 4 The Sperm Epigenome .................................................................................. 26 Forms and Functions of tRNA fragments ....................................................... 38 Regulation of Endogenous Retrovirus Family ERV-L .................................... 52 Cajal body and Histone Locus Body Functions ............................................. 64 Chapter II: Repression of endogenous retrovirus transcription by a tRNA fragment ........................................................................................................... 73 Abstract .......................................................................................................... 73 Introduction .................................................................................................... 73 Results ........................................................................................................... 77 Discussion ...................................................................................................... 96 Materials and Methods ................................................................................... 101 ix Chapter III: The molecular function of tRNA fragment Gly-GCC ................ 119 Abstract .......................................................................................................... 119 Introduction .................................................................................................... 119 Results ........................................................................................................... 122 Discussion ...................................................................................................... 140 Materials and Methods ................................................................................... 145 Chapter IV: Discussion ................................................................................... 158 Epididymosome epidemiological epigenomics .............................................
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