Life-spanning study of polycomb regulation by cohesin - the epigenome controls cell type-specific gene expression, establishing the diversity of cell types in the human body

However, over time, the epigenome becomes dysregulated, which promotes aging. Despite the tight link between epigenetics and aging, the mechanisms that preserve the epigenome in young cells and why these mechanisms degrade over time remain poorly understood. Polycomb-mediated gene repression maintains cell identity by silencing the genes that specify other cell types. As facultative heterochromatin, polycomb is highly dynamic during development, enabling differentiating stem cells to rapidly alter gene expression programs. However, polycomb switches from being flexible during development to becoming a stable mechanism of repression throughout adulthood. Understanding polycomb regulation is key to advancing our knowledge of aging, as disrupting polycomb components alters lifespan across various organisms. How polycomb repression is maintained in terminally differentiated cells remain unknown. However, studies in embryonic stem cells indicate that spatial organization of repressed sites is crucial, with polycomb-repressed regions forming ultra-long-range loops to sustain silencing. While these loops were thought to be solely mediated by polycomb complexes, preliminary work from the applicant shows that cohesin and ctcf (which facilitate long-range enhancer-promoter loops) also mediate repressive loops in embryonic stem cells. In the F99 phase of this proposal, performed at MIT, the applicant will use computational methods developed by the mirny and dekker labs to determine whether cohesin and ctcf-dependent looping is a broad regulatory mechanism of polycomb repression. Aim 1.1 will identify polycomb targets in embryonic stem cells that derepress when cohesin or ctcf is lost and aim 1.2 will use mechanistic polymer modeling to link cohesin and ctcf's roles in 3D looping activity to polycomb repression. In aim 1.3, machine learning and polymer modeling will predict how gene expression in different cell types, particularly mature hepatocytes, respond to site-directed ctcf perturbations. These insights will propel the applicant's transition to aging research, where she will test whether enhancing cohesin activity can protect polycomb repression in aging mouse livers (aim 2). The K00 phase will also use cutting-edge and single-cell experimental techniques to measure genome RE-organization as polycomb becomes dysregulated during the normal aging process. In addition to training in machine learning and hepatic chromatin, the applicant will gain expertise in aging research during the F99 stage through lab visits, conference attendance, and a course on aging and its diseases. This study will advance our understanding of aging by comprehensively investigating a new mechanism of polycomb regulation. Rejuvenating the epigenome is a promising strategy for reversing cellular aging, and this work will determine if targeting the 3D genome offers a new approach.