Epigenetics: A Gatekeeper to DNA Amplification and Replication Control.

DNA amplification is associated with pathological states such as neurological disorders, cardiac disease and cancer. At least 50% of the amplifications in cancer are transient extrachromosomal DNA (ecDNA). The transient behavior contributes to copy number plasticity, results in heterogeneous oncogene expression and alters therapeutic response. The unanswered question remains as to whether distinct mechanisms control ecDNA copy gains within cells and how they impact copy gain events associated with disease. Our laboratory aims to define the principles regulating selective DNA amplification and the associated plasticity, so we may control these events in disease. By resolving general mechanisms governing selective DNA amplifications, we will build a framework to further understand the molecular basis by which copy gains occur in neoplasia and other diseases. Recent studies have begun to uncover the importance of epigenetic states and histone lysine methyltransferases (KMTs) and demethylases (KDMs) in regulating extrachromosomal transient site-specific DNA copy number gains (TSSGs). In fact, our laboratory discovered the first chromatin factor promoting TSSGs in the human genome. We have revealed a critical interplay between a myriad of KMTs and KDMs in modulating methylation balance in order to control rereplication and extrachromosomal amplification events. The methyl-lysine modifier networks that control site-specific DNA amplification were resolved through genetic and chemical treatments coupled to cytological approaches, epigenomic profiling and 3D genome organizational analyses. While interrogating their role in controlling DNA amplification, we have also begun to appreciate their impact on chromatin modification dynamics and global DNA replication timing. We have established that enhancers coupled to methylation changes in broad methylation domains strongly predicts replication timing changes when perturbed by specific lysine modifiers. Taken together, we have established that methyl-lysine modifiers are key regulators promoting or preventing DNA amplification and play instrumental roles in regulating replication timing control through the combined regulation of methylation states. The most recent studies addressing these observations will be presented at the meeting.