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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network

ABSTRACT: Yeast cell cycle transcription dynamics in two S. cerevisae strains grown at 37Â°C: BF264-15DU (MATa ade1 his2 leu2-3, 112 trp1-1 ura3Dns, bar1) (wild type) and a mutant of the wild type strain lacking all Cdk1 activity, cdc28-4. We compared transcript levels of genes previously shown to be periodically expressed in wild-type cells (Orlando et al, 2008, Nature) to transcript levels in the absence of Cdk1 activity. Two replicate time courses from cells lacking all Cdk1 activity and one control time course from cells with wild-type Cdk1 activity are included.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Laura Simmons Kovacs

PROVIDER: E-GEOD-32974 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network.

Simmons Kovacs Laura A LA Mayhew Michael B MB Orlando David A DA Jin Yuanjie Y Li Qingyun Q Huang Chenchen C Reed Steven I SI Mukherjee Sayan S Haase Steven B SB

Molecular cell 20120202 5

During embryonic cell cycles, B-cyclin-CDKs function as the core component of an autonomous oscillator. Current models for the cell-cycle oscillator in nonembryonic cells are slightly more complex, incorporating multiple G1, S phase, and mitotic cyclin-CDK complexes. However, periodic events persist in yeast cells lacking all S phase and mitotic B-cyclin genes, challenging the assertion that cyclin-CDK complexes are essential for oscillations. These and other results led to the proposal that a n ...[more]

PMID: 22306294

Similar Datasets

Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network

Project description:Yeast cell cycle transcription dynamics in two S. cerevisae strains grown at 37°C: BF264-15DU (MATa ade1 his2 leu2-3, 112 trp1-1 ura3Dns, bar1) (wild type) and a mutant of the wild type strain lacking all Cdk1 activity, cdc28-4. We compared transcript levels of genes previously shown to be periodically expressed in wild-type cells (Orlando et al, 2008, Nature) to transcript levels in the absence of Cdk1 activity.

2012-02-03 | GSE32974 | GEO

Sodium arsenate response of wild type and slt2 deficient cells

Project description:Wild type (BY4741) Saccharomyces cerevisiae strains and their isogenic slt2 deficient counterparts, were treated for 2 hours with sodium arsenate 100 micromolar. Control (untreated) cells were also collected. Total RNA was extracted and analyzed by microarray hybridization. The data obtained from these experiments allows to determine those genes that are regulated by Slt2 activity after arsenate treatment. The experiments was designed as follows: Four types of samples were used: untreated wild type cells, treated wild type cells, untreated slt2- cells and treated slt2- cells. 3 independent replicates were performed for each experiment.

2010-07-25 | E-GEOD-17364 | biostudies-arrayexpress

Remodelling of whole-body lipid metabolism and a diabetic-like phenotype caused by loss of hepatic CDK1 and hepatocyte division

Project description:Purpose was to identify transcriptomic changes in whole liver and isolated hepatocytes from 12 month old wild type and Cdk1 liver-specific knock-out (Cdk1 Liv-/-) mice.

2020-10-14 | GSE159498 | GEO

Loss of hepatocyte cell division leads to liver inflammation and fibrosis

Project description:Purpose was to identify transcriptomic changes in whole liver and isolated hepatocytes from 2 week old wild type and Cdk1 liver-specific knock-out (Cdk1 Liv-/-) mice.

2020-10-14 | GSE159497 | GEO

Cdk1 controls global epigenetic landscape in embryonic stem cells

Project description:The cyclin-dependent kinase 1 (Cdk1) represents an ancient cell cycle kinase that has been conserved from yeast to humans. Cdk1 is the only essential mammalian Cdk, which drives cytokinesis by phosphorylating a large number of cellular proteins. To uncover additional functions of Cdk1, we generated a knock-in strain of mice expressing an analog-sensitive version of Cdk1 in place of wild-type Cdk1. These mice and cells derived from them allow us to investigate Cdk1 function in essentially any compartment and at any stage of development. In our study, we focused on embryonic stem (ES) cells, as this cell type expresses particularly high levels of Cdk1. Very unexpectedly, we found that in ES cells the majority of Cdk1 substrates are localized on chromatin. Cdk1 phosphorylates a large number of proteins involved in epigenetic regulation, including writers and erasers of all major histone marks. Consistent with this finding, inhibition of Cdk1 altered histone modification status of ES cells. High levels of Cdk1 in ES cells (and in induced pluripotent stem cells) phosphorylate and partially inactivate Dot1l, the histone H3 lysine 79 methyltransferase responsible for placing activating H3K79 marks on gene bodies. Decrease of Cdk1 activity during ES cell differentiation de-represses Dot1l, thereby allowing coordinated expression of differentiation genes. These analyses indicate that Cdk1 functions to maintain the epigenetic identity of ES cells.

2020-10-05 | PXD015173 | Pride

Regulation of S-phase transcription factors by Cdk1

2014-04-10 | GSE55121 | GEO

Regulation of S-phase transcription factors by Cdk1

Project description:Analysis of gene expression across the cell cycle from wild type cells, and cells expressing alleles of Yox1, Yhp1, Hcm1, and Tos4 that cannot be phosphorylated by Cdk1. Expression of S-phase and M/G1 transcripts are downregulated when phosphorylation of these factors is blocked, demonstrating that Cdk1 promotes expression of late cell cycle genes. These experiments are two-color hybridizations of RNA isolated from synchronized wild type (WT) or phosphomutant (4P) cells, compared to RNA from asyncrhonous wild type cells in mid-log phase. Wild type and mutant cells were synchronized in G1 phase, released into the cell cycle and samples collected at 15 minute intervals. Each time course was carried out in duplicate, the replicate experiment was performed as a dye swap.

2014-04-10 | E-GEOD-55121 | biostudies-arrayexpress

Mapping Replication Fork Pause Sites in S. cerevisiae

Project description:Replication forks face multiple obstacles that slow their progression. By two-dimensional gel analysis, yeast forks pause at stable DNA protein complexes, and this pausing is greatly increased in the absence of the Rrm3 helicase. We used a genome wide approach to identify 96 sites of very high DNA polymerase binding in wild type cells. Most of these binding sites were not previously identified pause sites. Rather, the most highly represented genomic category among high DNA polymerase binding sites was the open reading frames (ORFs) of highly transcribed RNA polymerase II genes. Twice as many pause sites were identified in rrm3 compared to wild type cells as pausing in this strain occurred at both highly transcribed RNA polymerase II genes and the previously identified protein DNA complexes. ORFs of highly transcribed RNA polymerase II genes are the first class of natural pause sites that are not exacerbated in rrm3 cells. We alse mapped pause sites using a second replication fork component, Rrm3-13MYC and got similar results. Genomic input (labelled with Cy3) and IP'ed DNA (labelled with Cy5) using a MYC Ab of either DNA Pol2-13MYC or Rrm3-MYC from asynchronously grown S. cerevisiae cells in rich media were hybridized to whole-genome PCR-based arrays containing ORF and intergenic regions of the entire genome (Ivery et al 2001). At least three biological replication and one technical replicate (dye swap) were performed. Log2 transformed median normalized ratios (IP/IN) were averaged for each experiment and significant peaks of either DNA Pol2 or Rrm3 association were identified

2009-06-15 | E-GEOD-16218 | biostudies-arrayexpress

Control of Cdc28 CDK1 by a stress-induced lncRNA

Project description:Genomic analysis has revealed the existence of a large number of long non-coding RNAs (lncRNAs) in a variety of organisms, including yeast. lncRNAs might have several biological functions during normal cell growth and development. Cells are subject to dramatic changes of gene expression in response to environmental changes. Using whole-genome tiling arrays, we found that a set of lncRNAs are induced specifically by the Hog1 stress-activated protein kinase (SAPK) in response to stress. Cdc28 kinase controls the cell cycle in yeast and there is a stress-induced lncRNA in the antisense orientation in CDC28, which permits Hog1 and RSC to induce CDC28 gene expression by remodeling the +1 nucleosome. Increased levels of Cdc28 mediate a more efficient cell cycle re-entry after stress. Therefore, Hog1 mediates changes on the level of Cdc28 protein by induction of a specific lncRNA.

2014-02-18 | E-MTAB-1686 | biostudies-arrayexpress

Global Control of cell cycle transcription by coupled CDK and network oscillators

Project description:Yeast cell cycle transcription dynamics in two S. cerevisae strains: BF264-15DU (MATa ade1 his2 leu2-3, 112 trp1-1 ura3Dns, bar1) [referred to as wild type] and a mutant of the wild type strain, clb1,2,3,4,5,6 GAL1-CLB1, [referred to as cyclin mutant] that does not express S-phase and mitotic cyclins. Both strains were synchronized by elutriation and released into YEP 2% dextrose/1M sorbitol at 30c. 15 samples were taken at 16 min intervals covering ~2 cycles in wild-type and ~1.5 cycles for the mutants. A significant fraction of the Saccharomyces cerevisiae genome is transcribed periodically during the cell division cycle, suggesting that properly timed gene expression is important for regulating cell cycle events. Genomic analyses of transcription factor localization and expression dynamics suggest that a network of sequentially expressed transcription factors could control the temporal program of transcription during the cell cycle. However, directed studies interrogating small numbers of genes indicate that their periodic transcription is governed by the activity of cyclin-dependent kinases (CDKs). To determine the extent to which the global cell cycle transcription program is controlled by cyclin/CDK complexes, we compared genome-wide transcription dynamics in wild type budding yeast to mutants that do not express S-phase and mitotic cyclins. Keywords: cell cycle, strain comparison

2008-05-07 | GSE8799 | GEO

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