The evolving mammalian 3D epigenome

One of life’s greatest mysteries is how a 6ft long-strand of DNA (our genome) fits inside the nucleus of a cell that’s less than a tenth of the width of a strand of hair. Adding to that, this genome has functioned faithfully with high fidelity over hundreds of millions of years of evolution is simply mind boggling. Moreover, within our genomes, we find millions of copies of strange genetic hitchhikers that were once thought to be purely self-seeking and parasitic. Critical advances in technology, assay development, sequencing, and computation have brought us today at an opportune moment in space and time, wherein we have the capabilities to probe, characterize and validate both the 3D folding of our genomes as well as these wandering snippets of DNA that hide in plain sight within our genome, formally known as transposable elements, or TEs in short.Predictably, a common thread that ties this dissertation together is TEs and the 3D epigenome, and the work presented here are composed of some equal as well as unequal parts of both. In the first and second chapters, I introduce a few core topics and some background reading for the work presented here. From the third chapter onwards, the work is presented in an almost chronological order and more coincidentally along the continuum of being TE-focused to 3D genome-focused. While this wasn’t specifically planned for, it accurately reflects the evolution of my research and interests during grad school and in the Wang Lab. In the third chapter, I started by examining the epigenomic landscape and the various regulatory roles TEs play in a large collection of human and mouse cell types. I leverage publicly available epigenomic datasets to synthesize the first, deeply annotated map of TEs detailing that their diverse roles have long been underreported. In the fourth chapter, I studied the evolution of chromatin looping in humans and mouse, discovered and validated a previously uncharacterized role of TEs in maintaining 3D genome folding. This work sheds light on TE’s contribution to regulatory plasticity by inducing redundancy and potentiating genetic drift locally while conserving genome architecture, showcasing a paradigm for defining regulatory conservation in the noncoding genome beyond classic sequence-level conservation. In the fifth chapter, I further report the role of TEs in contributing to 3D genome folding across a larger set of higher-order chromosomal structures in a greater collection of species and cell types. In sync with classical studies that highlight the novelty TEs bring to the host genome, we showcase and validate the role of TEs in creating novel, species-specific higher-order chromosomal structures leading to 3D epigenome rewiring and regulatory innovation. In chapter six and seven, I highlight a couple vignettes that arose from successful collaborations with researchers at UCSF and WashU. In the sixth chapter, we show that TEs may play an important role in the formation and evolution of super-interactive promoter groups in the developing human cortex. In the seventh chapter, we profiled the 3D local genome of the mouse Zeb2 locus and showed the importance of a critical fate-determining −165-kb enhancer in maintaining structural integrity. Lastly, in the eighth chapter, we show that combinatorial epigenetic therapy in a patient-derived glioblastoma stem cell model causes global remodeling of the epigenome and 3D genome organization—which we further dissect to show widespread changes in long- and short-range interactions that manifested in predominantly B to A compartment switching, loss of insulation and boundary strength at domain borders, and caused TADs to fuse. This work provides extensive preclinical evidence of dynamic changes in the physical packaging of the cancer genome upon treatment with epigenetic drugs. Over the last 2 decades, TEs have consistently shown up at the heart of important mysteries of life. The studies in this dissertation are no exception. Taken together, we characterize various new roles and functions of TEs in various settings: from cellular diversity to development to evolution of 3D genome over deep time, as well as in the response of 3D genome to therapeutic treatment of cancer, furthering their indisputable and indispensable role in cellular and mammalian evolution