Regulatory elements of replication timing and 3D genome organization

点击翻译按钮获取中文摘要

PROJECT SUMMARY Increasing evidence indicates that 3D genome architecture is required to regulate gene function and its alterations are associated with many diseases. The genome is organized into compartments that align with the temporal order of DNA replication (replication timing – RT). However, little is known about the mechanisms underlying RT control and 3D genome organization. Recently, we identified a novel class of cis regulatory elements that control RT and 3D genome organization: early replicating control elements – ERCEs. Our long-term goals are to study what are the regulatory elements of genome organization in human differentiated cell types, investigate how trans-acting factors control these elements, and define how 3D genome organization is remodeled during development and evolution. To achieve these goals, we are deleting and inserting candidate ERCEs into the genome of human differentiated cell types and testing their effects on RT, 3D genome organization and gene expression. We are also exploiting highly synchronous human embryonic stem cells differentiation systems to track ERCE activation during cell fate commitment. Finally, to better understand how the genome was remodeled during evolution, we are performing comparative analyses of 3D genome organization and function using primary cells derived from different species. In this project, we will exploit state-of-the-art genomic technologies combined with automated and scalable next-generation sequencing library preparation platforms to investigate the connections between RT, genome architecture and gene expression. Overall, we expect that our work will contribute significantly to understand the fundamental principles of genome organization and its relationship to gene function.