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The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Citation

L.B. Almeida, Bilena et al. (2022), The transcription factor network of E. coli steers global responses to shifts in RNAP concentration, Dryad, Dataset, 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 ja Aatos Erkon Säätiö, 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

Suomalainen Tiedeakatemia

Tampereen Yliopisto

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