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

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dc.contributor.affiliationTampere University - L.B. Almeida, Bilena
dc.contributor.affiliationTampere University - N.M. Bahrudeen, Mohamed
dc.contributor.affiliationTampere University - Chauhan, Vatsala
dc.contributor.affiliationTampere University - Dash, Suchintak
dc.contributor.affiliationUppsala University - Kandavalli, Vinodh
dc.contributor.affiliationUniversity of Helsinki - Häkkinen, Antti
dc.contributor.affiliationGoogle (United States) - Lloyd-Price, Jason
dc.contributor.affiliationTampere University - S.D. Palma, Cristina
dc.contributor.affiliationTampere University - S.C. Baptista, Ines
dc.contributor.affiliationUniversity of Connecticut - Gupta, Abhishekh
dc.contributor.affiliationTampere University - Kesseli, Juha
dc.contributor.affiliationTampere University - Dufour, Eric
dc.contributor.affiliationTallinn University of Technology - Smolander, Olli-Pekka
dc.contributor.affiliationTampere University - Nykter, Matti
dc.contributor.affiliationUniversity of Helsinki - Auvinen, Petri
dc.contributor.affiliationTampere University - T. Jacobs, Howard
dc.contributor.affiliationBoston University - M.D. Oliveira, Samuel
dc.contributor.affiliationTampere University - S. Ribeiro, Andre
dc.contributor.authorL.B. Almeida, Bilena
dc.contributor.authorN.M. Bahrudeen, Mohamed
dc.contributor.authorChauhan, Vatsala
dc.contributor.authorDash, Suchintak
dc.contributor.authorKandavalli, Vinodh
dc.contributor.authorHäkkinen, Antti
dc.contributor.authorLloyd-Price, Jason
dc.contributor.authorS.D. Palma, Cristina
dc.contributor.authorS.C. Baptista, Ines
dc.contributor.authorGupta, Abhishekh
dc.contributor.authorKesseli, Juha
dc.contributor.authorDufour, Eric
dc.contributor.authorSmolander, Olli-Pekka
dc.contributor.authorNykter, Matti
dc.contributor.authorAuvinen, Petri
dc.contributor.authorT. Jacobs, Howard
dc.contributor.authorM.D. Oliveira, Samuel
dc.contributor.authorS. Ribeiro, Andre
dc.date.accessioned2025-03-24T15:19:18Z
dc.date.issued2022-07-15
dc.date.issued2022-07-15
dc.descriptionThe 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.
dc.identifierhttps://doi.org/10.5061/dryad.wh70rxwnp
dc.identifier.urihttps://hydatakatalogi-test-24.it.helsinki.fi/handle/123456789/10503
dc.rightsOpen
dc.rights.licensecc-zero
dc.subjectGene Regulatory Networks
dc.subjectGenome-wide perturbations
dc.subjectTranscription
dc.subjectShort- and mid-term responses
dc.subjectTF regulatory effects
dc.titleThe transcription factor network of E. coli steers global responses to shifts in RNAP concentration
dc.typedataset
dc.typedataset

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