A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines

TL;DR

This study creates a comprehensive map of gene regulation in human stem cells using CRISPR and single-cell RNA sequencing, linking genetic variation to gene expression changes.

Contribution

The first genome-scale CRISPR interference map with single-cell RNA sequencing readouts across multiple genetic backgrounds in human pluripotent cells.

Findings

Knockdowns induce trans expression changes with mean and variance across donors.

Expression quantitative trait loci are linked to higher genetic modulation of perturbation effects.

The study provides experimental considerations for future population-scale CRISPR studies.

Abstract

Population-scale resources of genetic, molecular, and cellular information form the basis for understanding human genomes, charting the heritable basis of disease and tracing the effects of mutations. Pooled perturbation assays, probing the effect of many perturbations coupled with single-cell RNA sequencing (scRNA-seq) readout, are especially potent references for interpreting disease-linked mutations or gene-expression changes. However, the utility of existing maps has been limited by the comprehensiveness of perturbations conducted and the relevance of their cell-line context. Here, we present a genome-scale CRISPR interference perturbation map with scRNA-seq readout across many genetic backgrounds in human pluripotent cells. We map trans expression changes induced by knockdowns and characterize their variation across donors, with expression quantitative trait loci linked to higher genetic modulation of perturbation effects. This study pioneers population-scale CRISPR perturbations with high-dimensional readouts, which will fuel the future of effective modulation of cellular disease phenotypes.

•Combine natural genetic variation in healthy humans with single-cell CRISPR•Mean and variance in trans expression changes induced by knockdowns•eQTLs link to higher genetic modulation of perturbation effects•Experimental and technical considerations for conducting future population-scale studies

Combine natural genetic variation in healthy humans with single-cell CRISPR

Mean and variance in trans expression changes induced by knockdowns

eQTLs link to higher genetic modulation of perturbation effects

Experimental and technical considerations for conducting future population-scale studies

Feng et al. present the first genome-scale CRISPR interference perturbation map with scRNA-seq readout across many genetic backgrounds in human pluripotent cells, pioneering population-scale CRISPR perturbations with high-dimensional readouts, which will fuel the future of effective modulation of cellular disease phenotypes.

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