Genome-wide analysis of CRISPR perturbations indicates that enhancers act multiplicatively and without epistatic-like interactions

A single gene may have multiple enhancers, but how they work in concert to regulate transcription is poorly understood. To analyze enhancer interactions throughout the genome, we developed a generalized linear modeling framework, GLiMMIRS, for interrogating enhancer effects from single-cell CRISPR experiments. We applied GLiMMIRS to a published dataset and tested for interactions between 46,166 enhancer pairs and corresponding genes, including 264 high-confidence enhancer pairs. We found that enhancer effects combine multiplicatively but with limited evidence for further interactions. Only 31 enhancer pairs exhibited significant interactions (FDR < 0.1), of which none came from the high confidence subset and 20 were driven by outlier expression values. Additional analyses of a second CRISPR dataset and in silico enhancer perturbations with Enformer both support a multiplicative model of enhancer effects without interactions. Altogether, our results indicate that enhancer interactions are uncommon or have small effects that are difficult to detect. HighlightsO_LIAnalysis of a large single-cell CRISPRi screen finds limited evidence for synergistic or redundant interactions between enhancers C_LIO_LIThe collective action of multiple enhancers on a common target gene follows a multiplicative model of activity C_LIO_LIA new statistical framework for simulating and modeling data from single-cell CRISPRi screens C_LI