ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast.

Autor:	Mondeel TDGA; Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, Surrey, UK.; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands., Holland P; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE412 96, Sweden., Nielsen J; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE412 96, Sweden.; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK2800 Kgs., Denmark., Barberis M; Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, Surrey, UK.; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2019 Sep 05; Vol. 47 (15), pp. 7825-7841.
DOI:	10.1093/nar/gkz603
Abstrakt:	The understanding of the multi-scale nature of molecular networks represents a major challenge. For example, regulation of a timely cell cycle must be coordinated with growth, during which changes in metabolism occur, and integrate information from the extracellular environment, e.g. signal transduction. Forkhead transcription factors are evolutionarily conserved among eukaryotes, and coordinate a timely cell cycle progression in budding yeast. Specifically, Fkh1 and Fkh2 are expressed during a lengthy window of the cell cycle, thus are potentially able to function as hubs in the multi-scale cellular environment that interlocks various biochemical networks. Here we report on a novel ChIP-exo dataset for Fkh1 and Fkh2 in both logarithmic and stationary phases, which is analyzed by novel and existing software tools. Our analysis confirms known Forkhead targets from available ChIP-chip studies and highlights novel ones involved in the cell cycle, metabolism and signal transduction. Target genes are analyzed with respect to their function, temporal expression during the cell cycle, correlation with Fkh1 and Fkh2 as well as signaling and metabolic pathways they occur in. Furthermore, differences in targets between Fkh1 and Fkh2 are presented. Our work highlights Forkhead transcription factors as hubs that integrate multi-scale networks to achieve proper timing of cell division in budding yeast. (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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