Cell genomicsDec 2, 2025

A detailed single-cell map of gene regulation across human stem cell lines using CRISPR interference

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗

Updated Jun 27, 2026

Abstract

Essence

A population-scale CRISPRi map links gene knockdowns to trans expression effects across human pluripotent stem cell backgrounds.

Evidence

This genome-scale resource study used pooled CRISPR interference with single-cell RNA-seq readouts across many genetic backgrounds in human pluripotent cells.

Caveat

The abstract presents a reference map in pluripotent cell lines, so disease-phenotype modulation remains an inferred future use rather than a tested clinical outcome.

Simplified

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.