Regulation of gene transcription and DNA replication by chromatin readers from the BET family

Project Summary Precise and coordinated control of gene transcription and DNA replication is necessary for cell growth, proliferation, and differentiation. Dysregulation of transcription and DNA replication can result in transcription- replication conflicts and genome instability, often leading to cancer and other human diseases. Despite significant progress in understanding how transcription and DNA replication are regulated, the mechanisms responsible for coordinated control of these processes are largely unknown. Our research program aims to address this knowledge gap by combining our prior work on transcription with a new line of investigation into DNA replication. We will initially focus on elucidating the roles of chromatin readers from the bromodomain and extra-terminal domain (BET) family, which are known to be important regulators of transcription. BET proteins have additionally been implicated in DNA replication and the response to replication stress, but the mechanistic roles BET proteins play in these processes have not been determined. Our preliminary findings revealed that BET proteins are involved in DNA replication initiation. Building on this foundation, we are well-positioned to explore the fundamental mechanisms that regulate and coordinate transcription and DNA replication. We will focus on three broad research areas: 1) The roles of BET proteins in regulating a temporal program of origin activation. The temporal program of origin activation is important for avoiding transcription-replication conflicts. Our preliminary results illustrated that BET proteins facilitate the recruitment of a factor required for origin activation. We will build on these results to characterize the mechanisms of BET proteins in origin activation and in orchestrating the timing of origin firing. 2) The roles of BET proteins in managing transcription-replication conflicts. Prior studies and our preliminary data suggest that BET proteins are important for avoiding transcription-replication conflicts and mitigating their consequences. Here, we will characterize the roles of BET proteins in coordinating transcription and DNA replication and resolving transcription-replication conflicts. 3) Cell cycle-dependent interactions involving BET proteins. Based on current understanding, the complex roles of BET proteins are mediated through interactions with other factors, but the ensemble of BET protein partners remains to be determined. Prior studies and our preliminary data suggest that the composition of factors interacting with BET proteins may depend on the cell cycle stage and replication stress. Thus, we will define the BET protein interaction network and determine if and how this network changes during cell cycle progression and in response to replication stress. We will use a combination of genomic, proteomic, biochemical, and computational approaches to address these research areas. Our studies will advance current models of regulatory dynamics in the cell nucleus and facilitate the long-term growth of our research program toward a comprehensive understanding of the fundamental mechanisms that maintain the flow of genetic information and safeguard genome integrity.