Perturb-ME Maps Cell Mechanisms
Researchers from Genentech and the Broad Institute presented the Perturb-ME method in a preprint on August 18, which combines genome-wide CRISPR knockout with cell sorting and single-cell analysis to build maps of cell mechanisms. The approach combines genome-wide gene knockout with cell sorting by target protein level and simultaneous reading of the knocked-out gene, RNA, and surface markers in each cell.
In an experiment on melanoma cells, the authors reconstructed a regulatory network of 221 regulator genes and 1998 response genes, and deposited the code and computational pipelines in an open repository. The main obstacle in studying complex cellular processes remains the gap between arrays of genetic correlations and testable causal links. When biologists want to determine how each individual gene controls a trait, they have to choose between two extremes.
The new Perturb-ME approach (Perturb-seq with Marker Enrichment) overcomes this limitation with a two-step design. First, genes are knocked out across the genome in a pool of cells using the CRISPR system. Then, the population is passed through a flow cytometer, selecting only the top and bottom 5% of cells with the minimum and maximum levels of the protein of interest. This step filters out cells without an expressed response and concentrates the effective mutations.
Only after this cell sorting step are the cells sent for multimodal single-cell profiling. Within each cell, the guiding RNA, transcriptome, and level of surface proteins are read simultaneously using DNA-barcoded antibodies. The work of the method was verified using the example of the major histocompatibility complex I (MHC-I) in human melanoma cells, and the results were published in Nature Aging, July 2026.
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bioRxiv
Perturb-ME: Scalable mechanism discovery from phenotype-enriched genome-wide screens
Perturb-seq enables pooled genetic screens with rich single-cell profiling readouts, but genome-scale profiling remains costly and may not be associated with other established functional characteristics. Moreover, as screens grow in size and complexity, interpreting…
August 23, 2026 6
