UCLA Electronic Theses and Dissertations
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UCLA UCLA Electronic Theses and Dissertations Title Chromatin Architectural Dynamics in Cardiovascular Disease Permalink https://escholarship.org/uc/item/7wf4v4kp Author Chapski, Douglas Publication Date 2019 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Chromatin Architectural Dynamics in Cardiovascular Disease A dissertation suBmitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Molecular, Cellular, and Integrative Physiology by Douglas Chapski 2019 © Copyright By Douglas Chapski 2019 ABSTRACT OF THE DISSERTATION Chromatin Architectural Dynamics in Cardiovascular Disease by Douglas Chapski Doctor of Philosophy in Molecular, Cellular, and Integrative Physiology University of California, Los Angeles, 2019 Professor Thomas M. Vondriska, Chair The chromatin architectural rearrangements that permit disease gene expression are just Beginning to come to light. Distinct levels of chromatin organization are needed to maintain a healthy transcriptome, from the histone octamer that forms nucleosomes (the functional unit of chromatin) to chromosome territories that demarcate large swaths of the nucleus. An integrative picture of hoW each level of chromatin contriButes toWards healthy and disease gene expression has eluded us until chromosome conformation capture folloWed By high-throughput sequencing paved the Way for deeper study of hoW chromatin features, such as significant chromosomal interactions, topologically associating domains, A/B compartmentalization, and enhancer-gene interactions all contriBute toWards gene regulation at a gloBal scale. Heart failure is a syndrome ii characterized, in part, By a dysregulated gene expression program. We hypothesized that chromatin structure Becomes deranged during heart failure, and We found this to Be the case at multiple levels of chromatin organization. In addition, We found that healthy cardiac myocyte chromatin structure permits its organ-specific gene regulation program. This dissertation 1) summarizes the cardiovascular epigenetics Work in the field; 2) reports our findings from our chromosome conformation studies in hearts that underWent pressure overload and those that underWent knockout of the chromatin structural protein CTCF to understand hoW pathology influences chromatin structure; and 3) reports our investigation into the chromatin architectural organization of healthy cardiac myocytes When compared to healthy liver, in an effort to understand hoW normal epigenomes are organized in three dimensions. These studies open avenues for future mechanistic cardiovascular epigenomics studies, as Well as for exploration of therapeutic treatment of chromatin to promote healthier gene expression programs. iii The dissertation of Douglas Chapski is approved. Matteo Pellegrini James N. Weiss YiBin Wang Thomas M. Vondriska, Committee Chair University of California, Los Angeles 2019 iv This thesis is dedicated to my grandmother, Vitalina de Oliveira Carvalho, Who succumBed to heart failure during my PhD, and to the patients Who make our studies worth the journey. v TABLE OF CONTENTS ABstract of Dissertation ii Committee MemBers iv TaBle of Contents vi List of Figures vii List of TaBles ix AcknoWledgements x Biographical Sketch xiv Preface 1 Preface: BiBliography 4 Chapter 1: Epigenomes in Cardiovascular Disease 5 Chapter 1: BiBliography 65 Chapter 2: High resolution mapping of chromatin conformation in cardiac 101 myocytes reveals structural remodeling of the epigenome in heart failure Chapter 2: BiBliography 159 Chapter 3: Spatial Principles of Chromatin Architecture Associated With 169 Organ-Specific Gene Regulation Chapter 3: BiBliography 210 Future Directions: What’s Next for Cardiovascular Epigenomics 214 Future Directions: BiBliography 217 vi LIST OF FIGURES Figure 1-1: Occupancy of histone marks varies BetWeen cell types. 50 Figure 1-2: Chromatin conformation capture data reveal similarities in 51 chromatin organization BetWeen cell types. Figure 1-3: Chromatin looping. 53 Figure 1-4: Chromatin architectural features. 55 Figure 1-5: Plasticity in epigenomic landscapes may alloW for 57 transcriptome reprogramming in disease. Figure 1-6: Model for epigenomic changes in development and disease. 59 Figure 1-7: Cardiac epigenetic therapies. 60 Figure 2-1: Loss of CTCF induces cardiac pathology. 133 Figure 2-2: High-resolution cardiac chromatin conformation analyses 135 reveal changes in chromatin compartmentalization and gene expression in pressure overload and CTCF-KO mice. Figure 2-3: Short- and long-range chromatin interactions, and staBle 137 chromatin looping, are altered after pressure overload or CTCF-KO. Figure 2-4: Chromatin architecture is remodeled around cardiac genes 139 during disease. Figure 2-5: Three-dimensional interactions BetWeen enhancers and 141 genes are restructured after pressure overload or CTCF-KO. Figure 2-6: Model for epigenomic changes in development and disease. 143 Figure 2-7: Genome-Wide chromatin conformation capture datasets and 144 quality control analysis for Hi-C and RNA-seq. Figure 2-8: Generation and phenotypic characterization of cardiac- 146 specific CTCF knockout mice. Figure 2-9: CTCF expression is doWn-regulated By pathologic stress and 150 inversely correlated With heart size. Figure 2-10: Cardiac disease associated genes differentially expressed 152 after CTCF depletion. Figure 2-11: CTCF depletion does not promote apoptosis. 154 Figure 2-12: Human suBject clinical data. 155 Figure 2-13: Differences in Boundary strength and A/B 156 compartmentalization per chromosome. Figure 2-14: Implications for cardiac phenotype from chromatin structural 157 changes in TAC and CTCF-KO cardiac myocytes. Figure 3-1: Significant Fit-Hi-C interactions are oBserved in organ- 192 specific genes. Figure 3-2: Cardiac and liver genes are situated in open compartments. 193 Figure 3-3: Significant Fit-Hi-C interactions have a similar distriBution 195 among annotated features of the genome. Figure 3-4: Genes With promoter-TES loops tend to have organ-specific 197 functions Within the cell. vii Figure 3-5: Interchromosomal Fit-Hi-C interactions are preferentially 199 found at organ-specific genes. Figure 3-6: Interchromosomal Fit-Hi-C interactions Bridge regions of 200 differing A/B compartmentalization. Figure 3-7: 3D models of liver and heart genomes. 202 Figure 3-8: Properties of 3D models of heart and liver genomes. 203 Figure 3-9: Radial positions of TADs differ BetWeen heart and liver. 205 Figure 3-10: Comparison BetWeen contact proBaBility heatmaps from 206 experiment and structural models for heart (left) and liver (right). viii LIST OF TABLES TaBle 1-1. Gain/Loss of Function Studies on Chromatin Modifiers in the 61 Cardiovascular System. TaBle 1-2. List of genes With detected significant (q < 0.01 Fit-Hi-C 64 interactions BetWeen transcription start and end sites (shoWn in Figure 1-3). TaBle 3-1. Summary of Hi-C data from heart and liver 207 TaBle 3-2. List of genes With significant (q < 0.01) promoter-TES Fit-Hi-C 208 interactions in the heart TaBle 3-3. List of genes With significant (q < 0.01) promoter-TES Fit-Hi-C 209 interactions in the liver ix ACKNOWLEDGEMENTS First, I Would like to thank my PhD advisor, Dr. Thomas M. Vondriska, for his support during my doctoral studies. He took a chance on me When I Was first learning to analyze high-dimensional data, and it paid off: our Work has Become something to Be appreciated By those Who Wish to understand epigenomic mechanisms of heart failure. Tom has Been a key figure in the development of my thinking style, and his guidance With study design and experimental methodologies has proven invaluaBle. Importantly, he has taught me to navigate the World With poise and courtesy. Here I acknoWledge the profound impact that the memBers Vondriska LaB have made on me over the years. In particular, Dr. Manuel Rosa-Garrido has Been a mentor and friend Who never douBted my technical aBilities, even When conceptual and computational challenges appeared insurmountaBle. His relentless pursuit of chromatin structural insights is to Be admired. Maximilian CaBaj has provided a neW perspective on technical procedures in the laB, and has imparted Wholesome cultural Wisdom along the Way. Dr. Emma Monte taught me that science is not just aBout the results, But also about the questions that are asked. She can find holes in any ostensiBly airtight argument, and her sustained enthusiasm for science continues to Be an inspiration. Dr. Elaheh KarBassi has Been a Beacon of knoWledge With respect to chromatin structure in the cardiac myocyte, and has shoWn that one must have grit and a healthy supply of tenacity to make admiraBle achievements. Todd H. KimBall has provided consistent technical support With Wet laB experiments, and offered me the unique and exciting opportunity to help him With a x computational investigation of hoW Bird genomes are regulated during his initial graduate Work. His kindness and commitment to science are refreshing. All other laB memBers, past and present, have made true marks on me as a scientist and as a citizen of the world. Here I thank the journals Circulation Research, Circulation, and Frontiers in Cardiovascular Medicine, who allow us to use our open access, puBlished information in this dissertation. The Circulation Research paper (Chapter 1, puBlished in Circulation Research. 2018 May 25;122(11):1586-1607, PMID: 29798902) involved Manuel Rosa- Garrido