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Genome wide transcriptional oscillation for Saccharomyces cerevisiae CEN.PK122

ABSTRACT: Genetic and environmental stresses are known factors that influence an organisms phenotype. Time is rarely taken into consideration when studying phenotypic changes in cells. Time-resolved microarray data revealed genome-wide transcriptional changes in yeast strain CEN.PK122 oscillating with~2 periods. We mapped the global patterns of transcriptional oscillationsinto a 3-dimensional map to represent different cellular phenotypes ofoscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other.

ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe

PROVIDER: GSE30054 | GEO | 2012/04/17

SECONDARY ACCESSION(S): PRJNA144015

REPOSITORIES: GEO

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Genome wide transcriptional oscillation for Saccharomyces cerevisiae CEN.PK122

Project description:Genetic and environmental stresses are known factors that influence an organisms phenotype. Time is rarely taken into consideration when studying phenotypic changes in cells. Time-resolved microarray data revealed genome-wide transcriptional changes in yeast strain CEN.PK122 oscillating with~2 periods. We mapped the global patterns of transcriptional oscillationsinto a 3-dimensional map to represent different cellular phenotypes ofoscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other. High-resolution samples over time were collected for CEN.PK122 oscillating with 2 h period.

2012-04-16 | E-GEOD-30054 | biostudies-arrayexpress

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Project description:Genetic and environmental factors influence the phenotype of an organism. Time is rarely considered when studying changes in cellular phenotype. Time-resolved microarray data revealed genome-wide transcriptional changes in cells oscillating with ~2 and ~4 h periods. We mapped the global patterns of transcriptional oscillations into a 3-dimensional map to represent different cellular phenotypes of oscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other. Although cells differed in oscillation periods, transcripts involved in certain processes were conserved in a deterministic way. This ordered timing of biological process may allow cells to grow energetically efficient. Decreased glucose levels in the media were found to increase the redox cycles of yeast strain CEN.PK113-7D. Glucose may have acted as signaling molecules for timing longer catabolic processes in the cell population. As oscillation period lengthened, the peak to trough ratio of transcripts increased and the percent of cells in the unbudded (G0/G1) phase of the cell cycle increased. Gene transcripts appear to be coordinated with metabolic functions and the cell cycle. High-resolution samples over time were collected for CEN.PK113-7D oscillating with 4 hour period.

2012-04-16 | E-GEOD-30052 | biostudies-arrayexpress

Dynamics of two oscillation phenotypes in S. cerevisiae [2hr]

2012-04-16 | E-GEOD-30051 | biostudies-arrayexpress

Dynamics of two oscillation phenotypes in S. cerevisiae [4hr]

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Project description:Response of Saccharomyces cerevisiae engineered for xylose metabolism to changes in carbon source and aeration Keywords: ordered

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RRBS Profiling of Clonal Cell Lines with Different Circadian Period

Project description:Composed of negative feedback loops, circadian oscillations are thought to be noise-resistant. Yet, individual cells in culture are remarkably heterogenous, oscillating independently and with different period lengths. To assess whether differential methylation contributes to heritable heterogeneity of circadian periods, we used reduced representation bisulfite sequencing (RRBS) to explore DNA methylation profiles and their correlation with the transcriptome in the 10 clonal cell lines. To investigate the mechanisms underlying this heterogeneity, we generated and characterized hundreds of clonal cell lines from the same parent culture. By comparing clonal lines with different circadian periods, we identified a group of differentially methylated regions (DMRs).

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In-phase oscillation of global regulons is orchestrated by a pole-specific organizer

Project description:Cell fate determination in the asymmetric bacterium Caulobacter crescentus (Caulobacter) is triggered by the localization of the developmental regulator SpmX to the old (stalked) cell pole during the G1-S transition. While SpmX is required to localize and activate the cell fate-determining kinase DivJ at the stalked pole in Caulobacter, it is also required for organelle (stalk) positioning in the cousin Asticaccaulis. We unearth the conserved s54-dependent transcriptional activator regulator TacA as global regulator in Caulobacter whose activation by phosphorylation is indirectly down-regulated by SpmX. Using a combination of forward genetics and cytological screening we uncover a previously uncharacterized and polarized component (SpmY) of the TacA phosphorylation control system, and we show that the SpmY function and localization is conserved. Thus, we demonstrate that SpmX organizes a site-specific, ancestral and multi-functional regulatory hub whose function includes the coordinated control of two co-oscillating global transcriptional regulators, CtrA and TacA.

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The Oscillating miRNA 959-964 cluster impacts Drosophila feeding time and other circadian outputs.

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