Comprehensive CRISPRi Atlas Reveals Gene Functions in Human Stem Cells

Researchers have published a genome‑scale CRISPR interference (CRISPRi) atlas that maps the effects of silencing 11,692 expressed genes across more than 2.5 million single human induced pluripotent stem cells (iPSCs). The open‑access resource captures transcriptomic changes, allowing scientists to query how individual gene perturbations influence pluripotent identity, metabolism and self‑renewal. The study identified new regulators such as ZBTB41, a metabolic factor, and RNF7, which contributes to pluripotency, and highlighted the atlas as a “hypothesis engine” for stem‑cell research.

Senior author Prashant Mali said, “The result is a kind of reference atlas; it’s a way to look up what perturbing almost any gene does to a stem cell’s behavior.” Co‑first author Yesh Doctor added, “Scientists can use it to look up the functions of genes and build hypotheses on them instead of having to run the experiments themselves.” The dataset is also positioned to train AI models for genotype‑phenotype prediction and to support virtual disease modeling and target discovery.