Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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)

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE24770 | GEO | 2010/10/19

SECONDARY ACCESSION(S): PRJNA133379

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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, 157:53â61) Two biological replicates for each strain in a common reference design (no dye-swap)

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

Effect of loss of function of Gal11/Med15 and Med3 from the Mediator tail module in budding yeast

Project description:Gene expression was compared for wild type yeast (BY4741) and yeast lacking Gal11/Med15 and Med3, or from a gal11-myc med3∆ strain. The gal11-myc allele shows a partial loss of function when combined with med3∆. Expression was analyzed for yeast grown in YPD as well as in CSM. We also examined gene expression of the wild type strain BY4742 grown in YPD and include that data here.

2011-09-01 | GSE31774 | GEO

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

CEA SGF:E00013#yap1 aft W303a HU response

Project description:Analysis of the response to hydroxyurea in a yeast aft1 mutant strain compared to wild-type strain (BY4741 or BY4742 backgrounds). Cells were grown in YPD rich medium containong 200 mM hydroxyurea (HU) for 2 hours. Analysis of the response to hydroxyurea in a yeast aft1aft2 mutant strain (Y18aft2d) compared to wild-type strain (CM3260). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours. Gene expression changes due to the aft1 mutation were also analysed in absence of HU (BY4741 background). Analysis of mid-term response to hydroxyurea in a yeast wild-type strain (W303a). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours. Gene expression changes were analysed compared to the same strain grown in the same medium without HU. Keywords: repeat sample

2005-12-01 | GSE1914 | GEO

Effect of loss of function of Gal11/Med15 and Med3 from the Mediator tail module in budding yeast

Project description:Gene expression was compared for wild type yeast (BY4741) and yeast lacking Gal11/Med15 and Med3, or from a gal11-myc med3â strain. The gal11-myc allele shows a partial loss of function when combined with med3â. Expression was analyzed for yeast grown in YPD as well as in CSM. We also examined gene expression of the wild type strain BY4742 grown in YPD and include that data here. Gene expression was compared for wild type yeast (BY4741 and BY4742) and yeast lacking Gal11/Med15 and Med3, or from a gal11-myc med3â strain.

2011-08-31 | E-GEOD-31774 | biostudies-arrayexpress

CEA_SGF:E00015#aft_HU_response

Project description:Analysis of the response to hydroxyurea in a yeast aft1aft2 mutant strain (Y18aft2d) compared to wild-type strain (CM3260). Cells were grown in YPD rich medium containing 200 mM hydroxyurea (HU) for 2 hours. Gene expression changes due to the aft1 mutation were also analysed in absence of HU (BY4741 background). Keywords: repeat sample

2005-12-01 | GSE1942 | GEO

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 (Natural Strain Timecourse)

2010-10-19 | GSE24771 | GEO