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Data from: Decoupling transcription factor expression and activity enables dimmer switch gene regulation

Citation

Ricci-Tam, Chiara et al. (2021), Data from: Decoupling transcription factor expression and activity enables dimmer switch gene regulation, Dryad, Dataset, https://doi.org/10.5061/dryad.70rxwdbt3

Abstract

Gene-regulatory networks achieve complex mappings of inputs to outputs through mechanisms that are poorly understood. We found that in the galactose-responsive pathway in Saccharomyces cerevisiae, the decision to activate the transcription of genes encoding pathway components is controlled independently from the expression level, resulting in behavior resembling that of a mechanical dimmer switch. This was not a direct result of chromatin regulation or combinatorial control at galactose-responsive promoters; rather, this behavior was achieved by hierarchical regulation of the expression and activity of a single transcription factor. Hierarchical regulation is ubiquitous, and thus dimmer switch regulation is likely a key feature of many biological systems. Dimmer switch gene regulation may allow cells to fine-tune their responses to multi-input environments on both physiological and evolutionary time scales.

Usage Notes

Data is organized in .zip folders corresponding to Figures / Supplemental Figures from the associated publication, each containing a README.txt file and the relevant code in MATLAB (version R2019b), Python (version 3), or shell script necessary to reproduce the analysis and plots in those figures. With two exceptions noted below ([1] and [2]), each folder directly contains the relevant raw data files.

  • "Fig1_S1_S2.zip" - Figure 1, Figure S1, Figure S2
  • "Fig2a_FigS4dehijk" - Figure 2 panel A; Figure S4 panels D,E,H,I,J,K
  • "Fig2BC_S5CDEFG" - Figure 2 panels B,C; Figure S5 panels C,D,E,F,G
  • "Fig2d_S6ab" - Figure 2 panel D; Figure S6 panels A,B
  • "Fig2e" - Figure 2 panel E
  • "Fig4_S7" - Figure 4, Figure S7
  • "FigS3" - Figure S3
  • "FigS5_JKLMNO" - Figure S5 panels J,K,L,M,N,O
  • "FigS6_CDEFGH" - Figure S6 panels C,D,E,F,G,H

[1]: microscopy raw images associated with folder "Figure2d_S6ab.zip" are located in the parent Dryad directory in the following .zip folders:

  • "20201006 microscopy.zip" - microscopy dataset 1, 8hr timepoint
  • "20201007 microscopy.zip" - microscopy dataset 2, 8hr timepoint
  • "20201021 microscopy 8h.zip" - microscopy dataset 3, 8hr timepoint
  • "20201021 microscopy 24h 32h.zip" - microscopy dataset 3, 24hr and 32hr timepoints

[2]: raw sequencing read data files associated with folder "Fig2a_FigS4dehijk.zip" are located in the parent Dryad directory as .fastq.gz files: 

  • Sequencing run 1 (L93) files are named with the prefix "A_S###" where sample number ### is clarified by "L93_IDglobal.csv" and "Key.xlsx" in "Fig2a_FigS4dehijk.zip". "R1" and "R2" in file names designate paired end reads 1 and 2.
  • Sequencing run 2 (L108) files are named with the prefix "S###" where sample number ### is clarified by "L108_IDglobal.csv" and "Key.xlsx" in "Fig2a_FigS4dehijk.zip". "R1" and "R2" in file names designate paired end reads 1 and 2.

Funding

National Science Foundation, Award: DGE1144152

National Science Foundation, Award: 1349248

National Institutes of Health, Award: R01-GM120122-03