Maintenance of cellular memory during replication

PROJECT SUMMARY Regulation of genome access underlies development, differentiation, and response to stimuli. Genome access in turn is determined by nucleosome packaging and modification, the “chromatin landscape”. Static snapshots of the chromatin landscape cannot explain how stable cellular states arise despite constant chromatin dynamics. By developing new approaches in time-resolved structural epigenomics, we will uncover chromatin states that are invisible with current methods, to identify the molecular determinants of cellular identity. A key pathway that determines cellular identity during development is the polycomb pathway, an epigenetic mechanism of maintaining cell states through gene repression. By using our novel tools to track temporal dynamics of heterochromatin in unperturbed cells, we can map the recovery of heterochromatin after its dilution due to replication. We will identify the factors that determine the locations where polycomb enzymes are first recruited after replication. By tracking transcription and chromatin states across the cell cycle, we will identify bistable states of genes where they are expressed in one phase of the cell cycle, and they are packaged as heterochromatin in another phase of the cell cycle. Overall, our methods will resolve how the cell cycle influences chromatin states and how chromatin states in turn regulate the cell cycle. In summary, our approach of time-resolved- structural genomics will uncover not only the determinants of cellular memory in fundamental systems of mammalian development, but also provide the means to understand gene regulation across the cell cycle.