ArticleProceedings of the National Academy of Sciences of the United States of America2018
Distributed and dynamic intracellular organization of extracellular information.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Integrated transcriptomic and metabolomic analysis of the hypothalamic-pituitary-testicular axis in rooster lines with contrasting hatchability.Poultry science · 2026Article
- Twenty-Five Years of the Environmental Stress Response and the Enduring Power of Yeast in Stress Biology.Yeast (Chichester, England) · 2026Review
- Characterizing Optogenetic Tools for Use in Synthetic Gene Circuits.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Dynamic patterns of gene expression match extracellular signals through push-pull regulation.PLoS genetics · 2025Article
- Protocol for measuring the responses of multiple budding yeast strains to extracellular change in parallel using a microfluidic device.STAR protocols · 2025Article
- A two-step regulatory mechanism dynamically controls histone H3 acetylation by SAGA complex at growth-related promoters.Nucleic acids research · 2025Article
- Quantifying the nuclear localization of fluorescently tagged proteins.Bioinformatics advances · 2025Article
- The dependence of shugoshin on Bub1-kinase activity is dispensable for the maintenance of spindle assembly checkpoint response in Cryptococcus neoformans.PLoS genetics · 2025Article
- Dynamics of positional information in the vertebrate neural tube.Journal of the Royal Society, Interface · 2024Article
- FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi.PLoS computational biology · 2023Article
- Determining growth rates from bright-field images of budding cells through identifying overlaps.eLife · 2023Article
- Article
- An optimized reporter of the transcription factor hypoxia-inducible factor 1α reveals complex HIF-1α activation dynamics in single cells.The Journal of biological chemistry · 2023Article
- Article
- TORC1 and PKA activity towards ribosome biogenesis oscillates in synchrony with the budding yeast cell cycle.Journal of cell science · 2022Article
- DetecDiv, a generalist deep-learning platform for automated cell division tracking and survival analysis.eLife · 2022Article
- Quantifying information of intracellular signaling: progress with machine learning.Reports on progress in physics. Physical Society (Great Britain) · 2022Review
- Universal antigen encoding of T cell activation from high-dimensional cytokine dynamics.Science (New York, N.Y.) · 2022Article
- Cell cycle-independent integration of stress signals by Xbp1 promotes Non-G1/G0 quiescence entry.The Journal of cell biology · 2022Article
- Escherichia coli chemotaxis is information limited.Nature physics · 2021Article
Corrections and comments
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Authors and funding
6 authors.
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Abstract
Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.