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Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Saccharomyces cerevisiae Saccharomyces paradoxus

PROVIDER: GSE24772 | GEO | 2010/10/19

SECONDARY ACCESSION(S): PRJNA132217

REPOSITORIES: GEO

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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

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 (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 (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

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

2010-10-19 | GSE24770 | GEO

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

MRC1-dependent scaling of the budding yeast DNA replication timing program.

Project description:We describe the DNA replication timing programs of 14 yeast mutants with an extended S phase identified by a novel genome-wide screen. These mutants are associated with the DNA replication machinery, cell-cycle control, and dNTP synthesis and affect different parts of S phase. In 13 of the mutants, origin activation time scales with the duration of S phase. A limited number of origins become inactive in these strains, with inactive origins characterized by small replicons and distributed throughout S phase. In sharp contrast, cells deleted of MRC1, a gene implicated in replication fork stabilization and in the replication checkpoint pathway, maintained wild-type firing times despite over twofold lengthening of S phase. Numerous dormant origins were activated in this mutant. Our data suggest that most perturbations that lengthen S phase affect the entire program of replication timing, rather than a specific subset of origins, maintaining the relative order of origin firing time and delaying firing with relative proportions. Mrc1 emerges as a regulator of this robustness of the replication program.

| S-EPMC2877575 | biostudies-literature

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

Expansion of antisense lncRNA transcriptomes in budding yeast species since the loss of RNAi.

Project description:Antisense long noncoding RNAs (ASlncRNAs) have been implicated in regulating gene expression in response to physiological cues. However, little is known about the evolutionary dynamics of ASlncRNA and what underlies the evolution of their expression. Here, using budding yeast Saccharomyces spp. and Naumovozyma castellii as models, we show that ASlncRNA repertoires have expanded since the loss of RNA interference (RNAi), in terms of their expression levels, their lengths and their degree of overlap with coding genes. Furthermore, we show that RNAi is inhibitory to ASlncRNA transcriptomes and that increased expression of ASlncRNAs in the presence of RNAi is deleterious to N. castellii, which has retained RNAi. Together, our results suggest that the loss of RNAi had substantial effects on the genome-wide increase in expression of ASlncRNAs during the evolution of budding yeasts.

| S-EPMC4856548 | biostudies-literature

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