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| Status |
Public on Jun 07, 2022 |
| Title |
The transcription factor network of E. coli steers global responses to shifts in RNAP concentration |
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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.
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| Overall design |
GSE178279 [rich media] Examination of genome-wide responses under various media richness.
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| Contributor(s) |
L.B. Almeida B, N.M. Bahrudeen M, Chauhan V, Dash S, Kandavalli V, Häkkinen A, Lloyd-Price J, S.D. Palma C, S.C. Baptista I, Gupta A, Kesseli J, Dufour E, Smolander O, Nykter M, Auvinen P, T. Jacobs H, M.D. Oliveira S, S. Ribeiro A |
| Citation(s) |
35748858, 38687030 |
| |
| Submission date |
Jun 16, 2021 |
| Last update date |
Aug 09, 2024 |
| Contact name |
Andre Sanches Ribeiro |
| E-mail(s) |
andre.sanchesribeiro@tuni.fi
|
| Organization name |
Tampere University
|
| Department |
Faculty of Medicine and Health Technology
|
| Lab |
Laboratory of Biosystem Dynamics
|
| Street address |
Arvo Ylpön katu 34
|
| City |
Tampere |
| State/province |
Pirkanmaa |
| ZIP/Postal code |
33520 |
| Country |
Finland |
| |
|
| Platforms (1) |
| GPL24659 |
Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655) |
|
| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE178281 |
The transcription factor network of E. coli steers global responses to shifts in RNAP concentration |
|
| Relations |
| BioProject |
PRJNA738356 |
| SRA |
SRP324234 |
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