Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks
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...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022001088 |
| _version_ | 1797978240951779328 |
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| author | Matteo Barberis Thierry D.G.A. Mondeel |
| author_facet | Matteo Barberis Thierry D.G.A. Mondeel |
| author_sort | Matteo Barberis |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T05:20:37Z |
| format | Article |
| id | doaj.art-c18aae990fc641829eb7328b3caef6f9 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:20:37Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-c18aae990fc641829eb7328b3caef6f92022-12-24T04:51:54ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012017431751Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networksMatteo Barberis0Thierry D.G.A. Mondeel1Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK; Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, Surrey GU2 7XH, UK; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands; Corresponding author at: Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK.Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK; Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, Surrey GU2 7XH, UK; Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The NetherlandsTranscription 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.http://www.sciencedirect.com/science/article/pii/S2001037022001088Systems biologyNetworksTranscriptional regulationForkhead transcription factorsCell cycleMetabolism |
| spellingShingle | Matteo Barberis Thierry D.G.A. Mondeel Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks Computational and Structural Biotechnology Journal Systems biology Networks Transcriptional regulation Forkhead transcription factors Cell cycle Metabolism |
| title | Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks |
| title_full | Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks |
| title_fullStr | Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks |
| title_full_unstemmed | Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks |
| title_short | Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks |
| title_sort | unveiling forkhead mediated regulation of yeast cell cycle and metabolic networks |
| topic | Systems biology Networks Transcriptional regulation Forkhead transcription factors Cell cycle Metabolism |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022001088 |
| work_keys_str_mv | AT matteobarberis unveilingforkheadmediatedregulationofyeastcellcycleandmetabolicnetworks AT thierrydgamondeel unveilingforkheadmediatedregulationofyeastcellcycleandmetabolicnetworks |