Linking genotypes with multiple phenotypes in single-cell CRISPR screens

CRISPR/Cas9 based functional screening coupled with single-cell RNA-seq (“single-cell CRISPR screening”) unravels gene regulatory networks and enhancer-gene regulations in a large scale. We propose scMAGeCK, a computational framework to systematically identify genes and non-coding elements associated with multiple expression-based phenotypes in single-cell CRISPR screening. scMAGeCK identified genes and enhancers that modulate the expression of a known proliferation marker, MKI67 (Ki-67), a result that resembles the outcome of proliferation-linked CRISPR screening. We further performed single-cell CRISPR screening on mouse embryonic stem cells (mESC), and identified key genes associated with different pluripotency states. scMAGeCK enabled an unbiased construction of genotype-phenotype network, where multiple phenotypes can be regulated by different gene perturbations. Finally, we studied key factors that improve the statistical power of single-cell CRISPR screens, including target gene expression and the number of guide RNAs (gRNAs) per cell. Collectively, scMAGeCK is a novel and effective computational tool to study genotype-phenotype relationships at a single-cell level.