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Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes (Natural Strain Timecourse)

ABSTRACT: Multi-genome, time series transcriptome measurements across the budding yeast cell cycle 378 genome-wide microarray measurements, 18 timepoints, nine strains of S. cerevisiae and one strain of S. paradoxus

ORGANISM(S): Saccharomyces cerevisiae Saccharomyces paradoxus

PROVIDER: GSE24771 | GEO | 2010/10/19

SECONDARY ACCESSION(S): PRJNA133381

REPOSITORIES: GEO

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Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes (Natural Strain Timecourse)

Project description:Multi-genome, time series transcriptome measurements across the budding yeast cell cycle 378 genome-wide microarray measurements, 18 timepoints, nine strains of S. cerevisiae and one strain of S. paradoxus Dye-swap technical replication at each strain,timepoint pair in a common reference design

2010-10-19 | E-GEOD-24771 | biostudies-arrayexpress

Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes

Project description:This SuperSeries is composed of the following subset Series: GSE24770: Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes (Mutation Accumulation Lines) GSE24771: Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes (Natural Strain Timecourse) Refer to individual Series

2010-10-19 | E-GEOD-24772 | biostudies-arrayexpress

Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes.

Project description:BACKGROUND:Gene expression is a dynamic trait, and the evolution of gene regulation can dramatically alter the timing of gene expression without greatly affecting mean expression levels. Moreover, modules of co-regulated genes may exhibit coordinated shifts in expression timing patterns during evolutionary divergence. Here, we examined transcriptome evolution in the dynamical context of the budding yeast cell-division cycle, to investigate the extent of divergence in expression timing and the regulatory architecture underlying timing evolution. RESULTS:Using a custom microarray platform, we obtained 378 measurements for 6,263 genes over 18 timepoints of the cell-division cycle in nine strains of S. cerevisiae and one strain of S. paradoxus. Most genes show significant divergence in expression dynamics at all scales of transcriptome organization, suggesting broad potential for timing changes. A model test comparing expression level evolution versus timing evolution revealed a better fit with timing evolution for 82% of genes. Analysis of shared patterns of timing evolution suggests the existence of seven dynamically-autonomous modules, each of which shows coherent evolutionary timing changes. Analysis of transcription factors associated with these gene modules suggests a modular pleiotropic source of divergence in expression timing. CONCLUSIONS:We propose that transcriptome evolution may generally entail changes in timing (heterochrony) rather than changes in levels (heterometry) of expression. Evolution of gene expression dynamics may involve modular changes in timing control mediated by module-specific transcription factors. We hypothesize that genome-wide gene regulation may utilize a general architecture comprised of multiple semi-autonomous event timelines, whose superposition could produce combinatorial complexity in timing control patterns.

| S-EPMC3218661 | biostudies-literature

Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes (Mutation Accumulation Lines)

Project description:45 genome-wide microarray measurements for 23 mutation accumulation lines grown in YPD liquid culture MA lines obtained by single-colony transfer on YPD plates for 600 generations, starting from a BY4741 derived strain (see Zeyl C, DeVisser JA: Estimates of the rate and distribution of fitness effects of spontaneous mutation in Saccharomyces cerevisiae. Genetics 2001, 157:53–61)

2010-10-19 | GSE24770 | GEO

Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes (Mutation Accumulation Lines)

2010-10-19 | E-GEOD-24770 | biostudies-arrayexpress

Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes (Natural Strain Timecourse)

Project description:Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes (Natural Strain Timecourse)

| PRJNA133381 | ENA

Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes

Project description:This SuperSeries is composed of the SubSeries listed below.

2010-10-19 | GSE24772 | GEO

Conservation of replication timing reveals global and local regulation of replication origin activity.

Project description:DNA replication initiates from defined locations called replication origins; some origins are highly active whereas others are dormant and rarely used. Origins also differ in their activation time resulting in particular genomic regions replicating at characteristic times and in a defined temporal order. Here we report the comparison of genome replication in four budding yeast species: Saccharomyces cerevisiae, S. paradoxus, S. arboricolus and S. bayanus. First, we find that the locations of active origins are predominantly conserved between species, whereas dormant origins are poorly conserved. Second, we generated genome-wide replication profiles for each of these species and discovered that the temporal order of genome replication is highly conserved. Therefore, active origins are not only conserved in location, but also activation time. Only a minority of these conserved origins show differences in activation time between these species. To gain insight as to the mechanisms by which origin activation time is regulated we generated replication profiles for a S. cerevisiae / S. bayanus hybrid strain and find that there are both local and global regulators of origin function. Measurement of genome replication time from 4 budding yeast species (Saccharomyces cerevisiae, S. paradoxus, S. arboricolus and S. bayanus) and a hybrid (between Saccharomyces cerevisiae and S. bayanus). For each strain two samples were analysed: a replicating sample (from S phase) and a non-replicating sample (from G2 phase) The reference genome sequences for each yeast species are available as Series supplementary file [sac*.fa]

2012-06-19 | E-GEOD-36045 | biostudies-arrayexpress

Evolution of Translation Regulation in budding Yeast

Project description:Comparison of translation efficiency in S. cerevisiae, S. paradoxus, and their F1 hybrid.

2013-12-04 | GSE52119 | GEO

Budding yeast respiratory oscillations in a transient state

Project description:RNAseq analysis of budding yeast respiratory oscillations was performed at high temporal resolution (4 min, 24 samples), covering 2.5 cycles of the short period oscillation of the IFO 0233 strain of budding yeast. This and related systems were previously analyzed by microarrays and RNAseq, but the expression of noncoding transcripts has not been analyzed. The oscillations were recorded by online measurements and the system underwent a multi-generational transient, where periods first gradually decreased (from 0.7 h to 0.6 h), and then a bifurcation of system dynamics occurred. After this bifurcation periods were longer but the oscillation was unstable. The RNAseq samples were taken in the 2.5 cycles before this bifurcation occurred, i.e., the data provides a snapshot of a transient state of the respiratory oscillations.

2022-07-11 | E-MTAB-11901 | biostudies-arrayexpress

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