ArticleNature communications2025
Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Intestinal lipid metabolism controls molecular and behavioral immunity through NHR-68 and gut-brain signaling in Caenorhabditis elegans.PLoS biology · 2026Article
- Transcriptomic Insights into Developmental Toxicity of Per- and polyfluoroalkyl Substances (PFAS) inEnvironment & health (Washington, D.C.) · 2026Article
- A spatially coordinated keratinocyte-fibroblast circuit recruits MMP9Nature immunology · 2026Article
- An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal.Nucleic acids research · 2026Article
- MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation prediction.PLoS computational biology · 2026Article
- Distinct S-adenosylmethionine synthases link phosphatidylcholine to mitochondrial function and stress survival.PLoS biology · 2025Article
- P-glycoprotein-9-mediated multidrug tolerance in Caenorhabditis elegans.Parasites & vectors · 2025Article
- Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq.Nature communications · 2025Article
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Abstract
Transcriptomes provide highly informative molecular phenotypes that, combined with gene perturbation, can connect genotype to phenotype. An ultimate goal is to perturb every gene and measure transcriptome changes, however, this is challenging, especially in whole animals. Here, we present 'Worm Perturb-Seq (WPS)', a method that provides high-resolution RNA-sequencing profiles for hundreds of replicate perturbations at a time in living animals. WPS introduces multiple experimental advances combining strengths of Caenhorhabditis elegans genetics and multiplexed RNA-sequencing with a novel analytical framework, EmpirDE. EmpirDE leverages the unique power of large transcriptomic datasets and improves statistical rigor by using gene-specific empirical null distributions to identify DEGs. We apply WPS to 103 nuclear hormone receptors (NHRs) and find a striking 'pairwise modularity' in which pairs of NHRs regulate shared target genes. We envision the advances of WPS to be useful not only for C. elegans, but broadly for other models, including human cells.
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