Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

Replogle, J. M.; Saunders, R. A.; Pogson, A. N.; Hussmann, J. A.; Lenail, A.; Guna, A.; Mascibroda, L.; Wagner, E. J.; Adelman, K.; Bonnar, J. L.; Jost, M.; Norman, T. M.; Weissman, J. S.

doi:10.1101/2021.12.16.473013

bioRxiv · 10.1101/2021.12.16.473013

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

Replogle, J. M.·Saunders, R. A.·Pogson, A. N.·Hussmann, J. A.·Lenail, A.·Guna, A.·Mascibroda, L.·Wagner, E. J.·Adelman, K.·Bonnar, J. L.·Jost, M.·Norman, T. M.·Weissman, J. S.

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Abstract

A central goal of genetics is to define the relationships between genotypes and phenotypes. High-content phenotypic screens such as Perturb-seq (pooled CRISPR-based screens with single-cell RNA-sequencing readouts) enable massively parallel functional genomic mapping but, to date, have been used at limited scales. Here, we perform genome-scale Perturb-seq targeting all expressed genes with CRISPR interference (CRISPRi) across >2.5 million human cells and present a framework to power biological discovery with the resulting genotype-phenotype map. We use transcriptional phenotypes to predict the function of poorly-characterized genes, uncovering new regulators of ribosome biogenesis (including CCDC86, ZNF236, and SPATA5L1), transcription (C7orf26), and mitochondrial respiration (TMEM242). In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena - from RNA processing to differentiation. We leverage this ability to systematically identify the genetic drivers and consequences of aneuploidy and to discover an unanticipated layer of stress-specific regulation of the mitochondrial genome. Our information-rich genotype-phenotype map reveals a multidimensional portrait of gene function and cellular behavior.

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Replogle, J. M., Saunders, R. A., Pogson, A. N., Hussmann, J. A., Lenail, A., Guna, A., Mascibroda, L., Wagner, E. J., Adelman, K., Bonnar, J. L., Jost, M., Norman, T. M., Weissman, J. S.. 2021-12-17. Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq. https://doi.org/10.1101/2021.12.16.473013

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