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Identification of ploidy-regulated genes in budding yeast

ABSTRACT: Using RNA-seq, we analyzed the transcriptomes of isogenic haploid (MATa) and tetraploid (MATaaaa) budding yeast strains in the Sigma 1278b background and identified genes whose regulation was altered by ploidy. Analysis of poly(A)+ RNA from 2 biological replicates of haploid (MATa) and tetraploid (MATaaaa) strains.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Alex Rolfe

PROVIDER: E-GEOD-19685 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Control of transcription by cell size.

Wu Chia-Yung CY Rolfe P Alexander PA Gifford David K DK Fink Gerald R GR

PLoS biology 20101102 11

Cell size increases significantly with increasing ploidy. Differences in cell size and ploidy are associated with alterations in gene expression, although no direct connection has been made between cell size and transcription. Here we show that ploidy-associated changes in gene expression reflect transcriptional adjustment to a larger cell size, implicating cellular geometry as a key parameter in gene regulation. Using RNA-seq, we identified genes whose expression was altered in a tetraploid as ...[more]

PMID: 21072241

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Identification of ploidy-regulated genes in budding yeast

Project description:Using RNA-seq, we analyzed the transcriptomes of isogenic haploid (MATa) and tetraploid (MATaaaa) budding yeast strains in the Sigma 1278b background and identified genes whose regulation was altered by ploidy.

2010-11-04 | GSE19685 | GEO

Polyploidy can drive rapid adaptation in yeast

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Scaling of cellular processes with ploidy

Project description:While most eukaryotic cells are diploid, with two chromosome sets, variances in ploidy are common. Despite the relative prevalence of ploidy changes and their relevance for pathology and evolution, a complete picture of consequences of altered ploidy is missing. We analyzed transcriptome and proteome changes in budding yeast Saccharomyces cerevisiae from haploid to tetraploid and found that the mRNA and protein abundance increases linearly with ploidy, but does not double with doubling the DNA content. Besides this linear increase, we found that pathways related to mitochondria and to cytoplasmic ribosomes and translation are differentially regulated. Indeed, with increasing ploidy the cells reduce mitochondrial content and this effect can be rescued by antioxidants. Moreover, cells of higher ploidy reduce their ribosome content while maintaining constant translational output. We show that this is an active process regulated via the Tor1 and Sch9 kinases and a transcriptional corepressor of rDNA transcription, Tup1. Similarly, human tetraploid cells downregulate their ribosome content via Tle1, a Tup1 homolog, demonstrating that the proteome remodeling is a conserved response to increased ploidy.

2022-08-15 | PXD022605 | Pride

Schladebeck_Whi3_Ploidy

Project description:We analyzed and classified Whi3-regulated and ploidy-regulated genes in haploid and diploid strains of the Sigma1278b genetic background under vegetative growth conditions.<br><br>For this purpose, we measured transcriptional profiles of two different haploid MATa and one diploid MATa/a yeast strains of the following genotypes: WHI3 strain (SS_YHUM468=YHUM0468), whi3 strain (SS_ySS137=YHUM1920) and whi3-delta/whi3-delta strain (SS_ySS137dipl=YHUM2152). All three strains were grown in duplicate in YNB medium supplemented with tryptophan and uracil at 30 degrees C to an optical density of 1.0 before extraction of total RNA and transcriptional profiling<br><br>

2013-06-19 | E-MEXP-3610 | biostudies-arrayexpress

Polyploidy can drive rapid adaptation in yeast

Project description:Analysis of copy number variation in evolved haploid, diploid, tetraploid strains. All experimental samples were compared to the same reference strain S288C. The samples include the progenitor strains for the haploid, diploid, and tetraploid evolution experiments, and single colony isolates (clones) from the evolving populations at given time points. Evolved clones were analyzed at generation 250 unless the name is followed by gen35, gen55 or gen500, in which case those generations were analyzed.

2015-02-28 | E-GEOD-51017 | biostudies-arrayexpress

Scaling of cellular gene expression with ploidy

Project description:Whereas most eukaryotic cells are diploid, carrying two chromosome sets, variances in ploidy are common. Despite the relative prevalence of ploidy changes and their relevance for pathology and evolution, the consequences of altered ploidy for cellular gene expression remain poorly understood. We quantified changes in the transcriptome and proteome of the yeast Saccharomyces cerevisiae with different ploidy, from the haploid to the tetraploid state. We found that the abundance of proteins increases with ploidy, but does not scale proportionally with increasing DNA content, suggesting a compensatory, cellular response to increases in ploidy. We further found that pathways related to cytoplasmic ribosomes and translation are differentially regulated. With increasing ploidy the cells reduced the rRNA and ribosomal protein abundance, although they maintained a constant translational output. These adaptations stem from an active process that involves the kinases Tor1 and Sch9 and the transcriptional corepressor of rDNA transcription, Tup1. Consistent with our results in yeast, human tetraploid cells show reduced mTORC1 activity and downregulated their ribosome content via the Tup1 homolog Tle1, demonstrating that the proteome remodeling pathway discovered here constitutes a conserved response pathway to increased ploidy.

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Ploidy influences the cellular responses of gross chromosomal rearrangements in Saccharomyces cerevisiae

Project description:We investigated the effects of the ploidy on cellular response in strains carrying various types of gross chromosomal rearrangements. Fourteen mutated strains (6 haploid strains and 8 diploid strains) were compared to their associated parental strain (haploid or diploid parental strain). For each comparison, 2 microarray experiments implying biological replicates were performed.

2011-06-17 | E-GEOD-28285 | biostudies-arrayexpress

Transcription profiling by array of yeast haploid Sigma1278b wildtype strain and whi3 deletion strain

Project description:We determined and classified Whi3-regulated genes in haploid strains of the Sigma1278b genetic background under vegetative growth conditions. For this purpose, we measured transcriptional profiles of two different haploid MATa yeast strains of the following genotypes: WHI3 strain (468=YHUM0468) and whi3 strain (1105=YHUM1105).Both starins were grown in duplicate in YNB medium with tryptophan at 30°C to an optical density of 1.0 before extraction of total RNA and transcriptional profiling

2011-07-08 | E-MEXP-2810 | biostudies-arrayexpress

Transcription profiling of S. cerevisiae haploid Sigma1278b strains with msa1 or msa2 or tec1 deletions

Project description:We determined and classified Msa1-, Msa2- and Tec1-regulated genes in haploid strains of the Sigma1278b genetic background under vegetative growth conditions. For this purpose, we measured transcriptional profiles of five different haploid MATa yeast strains of the following relevant genotypes: (JvdF_94 = YHUM1694) control; (JvdF_64 = YHUM1864) msa1-delta; (JvdF_65 = YHUM1865) msa2-delta; (JvdF_19 = YHUM1900) msa1-delta msa2-delta; (JvdF_17 = YHUM1700) tec1-delta. All strains were grown in duplicate in SC medium lacking leucine and histidine at 30 degrees C to an optical density of 1.0 before extraction of total RNA and transcriptional profiling.

2013-10-25 | E-MEXP-3619 | biostudies-arrayexpress

Transcription profiling by array of yeast haploid Sigma1278b strains to detect Yak1-regulated genes

Project description:We determined and classified Yak1-regulated genes in haploid strains of the Sigma1278b genetic background under vegetative growth conditions. For this purpose, we measured transcriptional profiles of different haploid MATa yeast strains of the following genotypes:YAK1 (468=YHUM0468), yak1 (1313=YHUM1313), strain YHUM1313 (yak1) carrying a high copy plasmid with YAK1 (1313Yhc) and strain YHUM1313 (yak1) carrying a high copy plasmid with YAK1 K398R (1313KDhc). All strains were grown in duplicate in YNB medium supplemented with tryptophan at 30 degrees Celsius to an optical density of 1.0 before extraction of total RNA and transcriptional profiling.

2011-08-23 | E-MEXP-2885 | biostudies-arrayexpress

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