The organizing principle of chromatin architecture in three dimensions (3D) remains a major mystery in biology. A rapid progress has been made in the last decade to characterize the hierarchies of chromatin architecture, including enhancer-promoter loops, chromatin contact domains, topological domains and chromatin A/B com- partments. Importantly, the alteration of the 3D genome architecture plays an important role in human disease such as developmental disorders and cancer. However, a major current challenge is to determine the biologi- cal importance of each layer of these 3D chromatin architectures, to uncover their causative roles in modulat- ing gene expression and/or other nuclear activities, and to potentially manipulate these architectures for dis- ease intervention. We assembled a strong team of investigators to develop an innovative new toolset to help solve this challenge, which takes advantage of light controllable protein dimers and advanced Crispr/Cas9 ge- nome editing technology. Our goal in this project is to develop the prototype of this toolset that we referred to as PaCIR to create de novo enhancer-promoter loops and topological associated domain that could be rapidly activated and deactivated. The successful execution of this project will provide a highly demanded strategy to study chromatin loops at essentially any specific regions of interests in vitro and in vivo. This toolset is rapid, efficient and non-invasive, which will not only pave way for uncovering profound new insights into chromatin loops and domains in gene transcription control, but also shed lights on a novel concept to rectify disease- associated mal-formation of chromatin architectures.
Recent advances have uncovered a highly regulated chromatin organization in three dimensions in eukaryotes, the deregulation of which may underlie a large number of human diseases. However, a problem in studying and interpreting such chromatin organization lies in a lack of tools to conduct loss- or gain-of-function of specific chromatin loops. This proposal focuses on developing a new technology to address this problem, which will pave way for broad mechanistic studies of chromatin loops in determining gene expression and cell fate during development and diseases.