The propagation of perturbations in rewired bacterial gene networks.

Détails

Ressource 1Télécharger: Pub_NatCommun2015.pdf (1796.33 [Ko])
Etat: Public
Version: Final published version
ID Serval
serval:BIB_B9C508EF13FD
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
The propagation of perturbations in rewired bacterial gene networks.
Périodique
Nature Communications
Auteur(s)
Baumstark R., Hänzelmann S., Tsuru S., Schaerli Y., Francesconi M., Mancuso F.M., Castelo R., Isalan M.
ISSN
2041-1723 (Electronic)
ISSN-L
2041-1723
Statut éditorial
Publié
Date de publication
2015
Volume
6
Pages
10105
Langue
anglais
Résumé
What happens to gene expression when you add new links to a gene regulatory network? To answer this question, we profile 85 network rewirings in E. coli. Here we report that concerted patterns of differential expression propagate from reconnected hub genes. The rewirings link promoter regions to different transcription factor and σ-factor genes, resulting in perturbations that span four orders of magnitude, changing up to ∼ 70% of the transcriptome. Importantly, factor connectivity and promoter activity both associate with perturbation size. Perturbations from related rewirings have more similar transcription profiles and a statistical analysis reveals ∼ 20 underlying states of the system, associating particular gene groups with rewiring constructs. We examine two large clusters (ribosomal and flagellar genes) in detail. These represent alternative global outcomes from different rewirings because of antagonism between these major cell states. This data set of systematically related perturbations enables reverse engineering and discovery of underlying network interactions.

Mots-clé
Escherichia coli/genetics, Escherichia coli/metabolism, Escherichia coli Proteins/genetics, Escherichia coli Proteins/metabolism, Gene Expression Regulation, Bacterial, Gene Regulatory Networks, Promoter Regions, Genetic
Pubmed
Web of science
Open Access
Oui
Création de la notice
01/02/2017 21:09
Dernière modification de la notice
20/08/2019 15:27
Données d'usage