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Here, we devised a microfluidics system to characterize multiple phenotypes in single yeast cells over time before, during, and after salt stress. The system measured cell and colony size, growth rate, and cell-cycle phase along with nuclear trans-localization of two transcription factors: stress-activated Msn2 that regulates defense genes and Dot6 that represses ribosome biogenesis genes during an active stress response. By tracking cells dynamically, we discovered unexpected discordance between Msn2 and Dot6 behavior that revealed subpopulations of cells with distinct growth properties. Surprisingly, post-stress growth recovery was positively corelated with activation of the Dot6 repressor. In contrast, cells lacking Dot6 displayed slower growth acclimation, even though they grow normally in the absence of stress. We show that wild-type cells with a larger Dot6 response display faster production of Msn2-regulated Ctt1 protein, separable from the contribution of Msn2. These results are consistent with the model that transcriptional repression during acute stress in yeast provides a protective response, likely by redirecting translational capacity to induced transcripts.<\/jats:p>","DOI":"10.7554\/elife.82017","type":"journal-article","created":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T06:15:14Z","timestamp":1667974514000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.82017","source":"Crossref","is-referenced-by-count":12,"title":["Modeling single-cell phenotypes links yeast stress acclimation to transcriptional repression and pre-stress cellular states"],"prefix":"10.7554","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1295-7718","authenticated-orcid":true,"given":"Andrew C","family":"Bergen","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01y2jtd41","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Genomic Science Innovation, University of Wisconsin-Madison","place":["Madison, United 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