Developing next-generation high-content image-based genetic screens for multi-omic spatial phenotypes

Project Summary/Abstract Spatial organization of the genome, nucleome and transcriptome is key to their control of many essential genomic and cellular functions. Yet existing tools limit our ability to identify regulators of these spatial organizations. We are developing a high-content, image-based CRISPR screen to discover three-dimensional (3D) genome regulators, a first-in-kind technology to uncover the regulatome of 3D genome architectures across multiple length scales. Our proof-of-concept screen targeting hundreds of candidate regulators identified many novel chromatin organization regulators. The goal of this application is to advance our technology to develop a highly-efficient, large scale, and multi-omic screening platform to discover the molecular regulators of the spatial genome, nucleome and transcriptome. In Aim 1, we will develop a generalizable, large scale screening platform compatible with in situ spatial omics techniques. In Aim 2, we will develop multimodal detection and perturbation methods for comprehensive large scale screens of 3D nucleome regulators. In Aim 3, we will develop integrative methods for large scale screens of spatial transcriptome phenotypes to allow efficient discovery of the regulatory mechanisms of subcellular RNA transport and localization. We expect that these proposed developments will provide the research field with brand-new, broadly applicable technologies for mechanistic studies of the spatial genome, nucleome and transcriptome in a wide range of biomedical contexts.