Nadal-Ribelles, MarionaSolé, CarmeDíez Villanueva, PabloStephan-Otto Attolini, CamilleMatas, YaimaSteinmetz, Lars M.Nadal Clanchet, Eulàlia dePosas Garriga, Francesc2025-05-082025-05-082025Nadal-Ribelles M, Solé C, Díez-Villanueva A, Stephan-Otto Attolini C, Matas Y, Steinmetz L, et al. A single-cell resolved genotype-phenotype map using genome-wide genetic and environmental perturbations. Nat Commun. 2025 Mar 18;16(1):2645. DOI: 10.1038/s41467-025-57600-42041-1723http://hdl.handle.net/10230/70326Heterogeneity is inherent to living organisms and it determines cell fate and phenotypic variability. Despite its ubiquity, the underlying molecular mechanisms and the genetic basis linking genotype to-phenotype heterogeneity remain a central challenge. Here we construct a yeast knockout library with a clone and genotype RNA barcoding structure suitable for genome-scale analyses to generate a high-resolution single-cell yeast transcriptome atlas of 3500 mutants under control and stress conditions. We find that transcriptional heterogeneity reflects the coordinated expression of specific gene programs, generating a continuous of cell states that can be responsive to external insults. Cell state plasticity can be genetically modulated with mutants that act as state attractors and disruption of state homeostasis results in decreased adaptive fitness. Leveraging on intra-genetic variability, we establish that regulators of transcriptional heterogeneity are functionally diverse and influenced by the environment. Our multimodal perturbation-based single-cell Genotype-to-Transcriptome Atlas in yeast provides insights into organism-level responses.application/pdfeng© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.info:eu-repo/semantics/articlehttp://dx.doi.org/10.1038/s41467-025-57600-4Gene expressionGene expression analysisTranscriptomicsinfo:eu-repo/semantics/openAccess