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Histone Deacetylase 3 and the Epigenomic Regulation of Brown Adipose Physiology University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2017 Histone Deacetylase 3 And The Epigenomic Regulation Of Brown Adipose Physiology Matthew Joseph Emmett University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Genetics Commons, Molecular Biology Commons, and the Physiology Commons Recommended Citation Emmett, Matthew Joseph, "Histone Deacetylase 3 And The Epigenomic Regulation Of Brown Adipose Physiology" (2017). Publicly Accessible Penn Dissertations. 2851. https://repository.upenn.edu/edissertations/2851 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2851 For more information, please contact [email protected]. Histone Deacetylase 3 And The Epigenomic Regulation Of Brown Adipose Physiology Abstract Brown adipose tissue (BAT) is a thermogenic organ, which helps to protect body temperature against cold and can counteract metabolic disease. Numerous pathways modulate the activity of BAT in a highly regulated and coordinated manner to exert tight control over its immense calorie burning capacity. However, less is known regarding the transcriptional and epigenomic mechanisms controlling the thermogenic gene program of brown adipocytes. Here, we show that histone deacetylase 3 (HDAC3) is required for the activation of BAT enhancers to ensure thermogenic aptitude, thus enabling survival of dangerously cold environmental temperature. Loss of HDAC3 leads to deficient expression of uncoupling protein 1 (UCP1) and oxidative phosphorylation genes, resulting in an inability to survive severely cold temperatures. Mechanistic studies demonstrate BAT HDAC3 functions as a coactivator of the nuclear receptor estrogen-related receptor α (ERRα), through deacetylation of PGC-1α to promote enhancer activation and gene transcription. Remarkably, this coactivator function of HDAC3 is required for the basal expression of the thermogenic gene program and occurs independently of adrenergic signaling. Thus, HDAC3 primes Ucp1 and the thermogenic transcriptional program to maintain a critical capacity for BAT to enable survival of dangerously cold temperature. We further demonstrate that short environmental exposure to a moderate cold temperature circumvents the genetic requirement of HDAC3 for Ucp1 transcriptional activation. Environmental exposure facilitates a persistent epigenomic rescue mechanism permitting the prolonged expression of thermogenic genes and an acquired BAT aptitude to avert hypothermia. Notably, we discovered that moderate cold activates BAT ERRα enhancers in an HDAC3-independent manner. Together, these studies identify for the first time, that BAT HDAC3 coactivation of ERR enhancers promotes a basal thermogenic transcriptional program ensuring cold survival, while HDAC3-independent mechanisms, signaling from a moderate cold environment to genes, imparts epigenomic changes to influence the BAT thermogenic capacity against probable and impending dangerously cold temperatures. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Mitchell A. Lazar Keywords brown adipose, enhancer RNAs, epigenomic, HDAC3, metabolism, PGC-1a Subject Categories Genetics | Molecular Biology | Physiology This dissertation is available at ScholarlyCommons: https://repository.upenn.edu/edissertations/2851 HISTONE DEACETYLASE 3 AND THE EPIGENOMIC REGULATION OF BROWN ADIPOSE PHYSIOLOGY Matthew J. Emmett A DISSERTATION in Cell and Molecular Biology Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy 2017 Supervisor of Dissertation _________________________ Mitchell A. Lazar, M.D., Ph.D. Willard and Rhoda Ware Professor in Diabetes and Metabolic Diseases Graduate Group Chairperson _________________________ Daniel S. Kessler, Ph.D. Associate Professor of Cell and Developmental Biology Dissertation Committee Patrick Seale, Ph.D. (Chair), Associate Professor of Cell and Developmental Biology Kathryn E. Wellen, Ph.D., Associate Professor of Cancer Biology M. Celeste Simon, Ph.D., Arthur H. Rubenstein, MBBCh Professor Daniel J. Rader, M.D., Seymour Gray Professor of Molecular Medicine HISTONE DEACETYLASE 3 AND THE EPIGENOMIC REGULATION OF BROWN ADIPOSE PHYSIOLOGY COPYRIGHT 2017 Matthew Joseph Emmett This work is licensed under the Creative Commons Attribution- NonCommercial-ShareAlike 3.0 License To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/3.0/us/ To my wife, Jaclyn. iii ACKNOWLEDGMENT To Mitch Lazar: First and foremost, I would like to thank you for providing outstanding mentorship since the first day I arrived in your lab. Thank you for creating an unparalleled environment in which to learn, explore, and dive deeply into research. You continually answered questions, proposed and challenged ideas, and provided immense support. It has been a true pleasure to learn from you and have you as my PhD thesis advisor. I look forward to your continued mentorship through the exciting future stages of my education and career. To my PhD Thesis Committee: Patrick Seale, Kathryn Wellen, Celeste Simon, and Dan Rader. Thank you for all being excellent scientific role models and for your willingness to both support and challenge me. Our thesis committee meetings facilitated many insightful discussions, which helped shape the direction of my work. To Patrick- thank you for being an excellent committee chair. Your advice, and countless discussions regarding experiments, ideas, and science, has been outstanding. Your positivity and encouragement will stick with me far beyond my years in graduate school! To Zachary Gerhart-Hines: Thank you for the unwavering support and intellectual discussions. I’ve greatly enjoyed both your mentorship and friendship in the Lazar lab and from abroad in Copenhagen. To David Steger, Daniel Cohen, and Sean Armour: Thank you for our daily interactions that have furthered my development. I cannot thank each of you enough for the countless scientific questions and discussions, which have increased and broadened my understanding of science. To Dave, thank you for all of the personal support and iv discussions over the past few years. Your mentorship and advice was terrific, as well as your occasional joke. To Lim: Thank you for an excellent collaboration spanning several years and the achievements that we’ve had together. Your approach to bioinformatics and biology has informed my thinking, future research, and approach to collaborating. To Erika and Lindsey: Thank you for the unwavering support and friendship. We’ve had a lot of fun along the way! It has been a long road and I couldn’t have done it without your wonderful help and expert abilities. To Joe: Thank you for facilitating so much of the work that I was able to complete in the lab. Whenever I needed your help or assistance, you were there without question. To Hannah: Thank you for being an excellent learner, collaborator, and friend. It was a pleasure to teach you in the lab! To the remaining Lazar lab members, past and present: Thank you for the memories, fun times, and for sharing intellectual challenges and ideas. To the Penn MSTP: Many thanks to Skip Brass, Maggie Krall and my MSTP classmates, for always promoting each other and for being an inspirational group of people. To my past scientific mentors: Leisha Emens (Johns Hopkins), Elissa Lei (NIH), Ben Stanger (Penn), and Andrew Rhim (MD Anderson). Thank you for cultivating my scientific curiosity, potential, my growth, as well as the support along the way. To my family: Most importantly, thank you to my wife, Jaclyn, for the unending love, support, encouragement, patience, and constant fun. Thank you to my parents, for v always encouraging me to pursue ideas, aspirations, and for supporting my endeavors. Krista, Mark, and Saxby- thank you for your understanding, encouragement, and support. To the Bassett family, thank you for your unwavering support, encouragement, and sense of humor. vi ABSTRACT HISTONE DEACETYLASE 3 AND THE EPIGENOMIC REGULATION OF BROWN ADIPOSE PHYSIOLOGY Matthew Joseph Emmett Mitchell A. Lazar Brown adipose tissue (BAT) is a thermogenic organ, which helps to protect body temperature against cold and can counteract metabolic disease. Numerous pathways modulate the activity of BAT in a highly regulated and coordinated manner to exert tight control over its immense calorie burning capacity. However, less is known regarding the transcriptional and epigenomic mechanisms controlling the thermogenic gene program of brown adipocytes. Here, we show that histone deacetylase 3 (HDAC3) is required for the activation of BAT enhancers to ensure thermogenic aptitude, thus enabling survival of dangerously cold environmental temperature. Loss of HDAC3 leads to deficient expression of uncoupling protein 1 (UCP1) and oxidative phosphorylation genes, resulting in an inability to survive severely cold temperatures. Mechanistic studies demonstrate BAT HDAC3 functions as a coactivator of the nuclear receptor estrogen- related receptor α (ERRα), through deacetylation of PGC-1α, to promote enhancer activation and gene transcription. Remarkably, this coactivator function of HDAC3 is required for the basal expression of the thermogenic gene program and occurs independently of adrenergic signaling. Thus, HDAC3 primes Ucp1 and the thermogenic vii transcriptional program to maintain
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