The transcription factor network of E. coli steers global responses to shifts in RNAP concentration
Cite this dataset
L.B. Almeida, Bilena et al. (2022). The transcription factor network of E. coli steers global responses to shifts in RNAP concentration [Dataset]. Dryad. https://doi.org/10.5061/dryad.wh70rxwnp
Abstract
The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene’s numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.
Methods
Collection and data generation are described in the Methods sections of the main manuscript.
Data processing methods and the software packages used are described in the Methods sections of the main manuscript.
Funding
Jane and Aatos Erkko Foundation, Award: 10-10524-38
Finnish Cultural Foundation, Award: 50201300
Finnish Cultural Foundation, Award: 00200193
Finnish Cultural Foundation, Award: 00212591
EDUFI Fellowship, Award: TM-19-11105
Finnish Academy of Science and Letters
Tampere University
TTU development program 2016–2022, Award: 2014-2020.4.01.16-0032
Academy of Finland, Award: 307856
Academy of Finland, Award: 323576
Academy of Finland, Award: 322927
Academy of Finland, Award: 272376
Academy of Finland, Award: 256615