Spatial multiomic mapping of gene function with CRISPRoff

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PROJECT SUMMARY / ABSTRACT A hallmark goal in human biology is to define the relationship between genes and phenotypes. Mapping the function of every gene in human cells will enable us to begin to define how gene expression programs impart specialized and adaptive human cellular functions required for life. We are especially interested in how transcription factors and epigenetic regulators enact cell type specific gene expression programs to dictate cell function during early development. Elucidating how individual genes function to regulate transcription and thus to program cell phenotypes will transform our understanding of human biology, development and disease. A mechanistic understanding of gene function requires scalable approaches for perturbing gene activity, single cell molecular phenotyping assays and robust models of human multicellular biology. We recently developed CRISPRoff— a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that durably and robustly silences gene expression. Unlike CRISPR mutagenesis approaches, CRISPRoff gene silencing effectively programs null alleles at the level of target gene mRNA and protein in polyclonal cell populations without induction of DNA damage or the unpredictability of DNA repair processes. We are proposing to optimize a generalizable multiomic CRISPRoff platform for molecularly phenotyping null alleles at single-cell resolution in multicellular models of human development. We will then use this CRISPRoff platform to create single-cell molecular multiomic maps of nuclear gene function across space and time. Lastly, we will evaluate genetic compensation and paralog functional redundancy in multicellular models. Our proposed research will serve to demonstrate the utility of this multiomics CRISPRoff platform for characterizing null alleles and motivate extending this approach to functionally map null allele phenotypes for all genes encoded by the human genome. The results of the proposed research will serve as a fundamental resource and roadmap for a broad community of biomedical scientists and greatly inform our understanding of gene function in human biology and disease.