This is the code repository for the computational analyses featured in:
Matteo Barberis, Thierry D.G.A. Mondeel, Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks, Computational and Structural Biotechnology Journal, 2022.
See https://doi.org/10.1016/j.csbj.2022.03.033 for the full publication.
Transcription factors are regulators of the cell’s genomic landscape. By switching single genes or entire molecular pathways on or off, transcription factors modulate the precise timing of their activation. The Forkhead (Fkh) transcription factors are evolutionarily conserved to regulate organismal physiology and cell division. In addition to molecular biology and biochemical efforts, genome-wide studies have been conducted to characterize the genomic landscape potentially regulated by Forkheads in eukaryotes. Here, we discuss and interpret findings reported in six genome-wide Chromatin ImmunoPrecipitation (ChIP) studies, with a particular focus on ChIP-chip and ChIP-exo. We highlight their power and challenges to address Forkhead-mediated regulation of the cellular landscape in budding yeast. Expression changes of the targets identified in the binding assays are investigated by taking expression data for Forkhead deletion and overexpression into account. Forkheads are revealed as regulators of the metabolic network through which cell cycle dynamics may be temporally coordinated further, in addition to their well-known role as regulators of the gene cluster responsible for cell division.
Keywords: Systems biology; Networks; Transcriptional regulation; Forkhead transcription factors; Cell cycle; Metabolism