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Omics score: 4

Expression data from Saccharomyces cerevisiae strains deleted for the THSC/TREX-2 subunits Thp1, Sac3 and Sus1

ABSTRACT: Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with a suboptimal assembly of the nascent messenger ribonucleo-protein particle (mRNP), as THO/TREX and the NPC-associated THSC/TREX-2 complex. We used microarrays to analyze the global impact of THSC/TREX-2 in gene expression and found that Thp1 and Sac3 depletion has a functional impact in highly-expressed, long and G+C-rich genes regardless of their function S. cerevisiae strains were grown in YPD liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays

OTHER RELATED OMICS DATASETS IN: PRJNA244324PRJNA244327PRJNA244325

PROVIDER: E-GEOD-56702 | ExpressionAtlas | 2015-08-04

REPOSITORIES: ExpressionAtlas

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A genome-wide function of THSC/TREX-2 at active genes prevents transcription-replication collisions.

Santos-Pereira José M JM García-Rubio María L ML González-Aguilera Cristina C Luna Rosa R Aguilera Andrés A

Nucleic acids research 20141007 19

The THSC/TREX-2 complex of Saccharomyces cerevisiae mediates the anchoring of transcribed genes to the nuclear pore, linking transcription elongation with mRNA export and genome stability, as shown for specific reporters. However, it is still unknown whether the function of TREX-2 is global and the reason for its relevant role in genome integrity. Here, by studying two TREX-2 representative subunits, Thp1 and Sac3, we show that TREX-2 has a genome-wide role in gene expression. Both proteins show ...[more]

PMID: 25294824

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Expression data from Saccharomyces cerevisiae strains deleted for the THSC/TREX-2 subunits Thp1, Sac3 and Sus1

Project description:Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with a suboptimal assembly of the nascent messenger ribonucleo-protein particle (mRNP), as THO/TREX and the NPC-associated THSC/TREX-2 complex. We used microarrays to analyze the global impact of THSC/TREX-2 in gene expression and found that Thp1 and Sac3 depletion has a functional impact in highly-expressed, long and G+C-rich genes regardless of their function S. cerevisiae strains were grown in YPD liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays

2014-10-08 | E-GEOD-56702 | biostudies-arrayexpress

Expression data from Saccharomyces cerevisiae strains deleted for different subunits of the THO/TREX complex

Project description:THO/TREX is a conserved nuclear complex that functions in mRNP biogenesis at the interface of transcription-RNA export with a key role in preventing transcription-associated genome instability. We used microarrays to analyze the impact of different THO/TREX mutations on gene expression and found that THO-Sub2 deletions have a high functional impact on highly expressed, long and G+C-rich genes regardless of gene function. S. cerevisiae strains were grown in YPAD liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays.

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Expression data from Saccharomyces cerevisae strains deleted for the RNA-binding hnRNP Npl3

Project description:Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with a suboptimal assembly of the nascent messenger ribonucleo-protein particle (mRNP), as THO/TREX and some heterogeneous nuclear ribonucleoproteins (hnRNPs) mutants. We used microarrays to the global impact of Npl3 in gene expression and found that Npl3 deletion has a functional impact in highly-expressed, long and G+C rich genes regardless of gene function. S. cerevisiae strains were grown in YPD liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays.

2013-11-15 | E-GEOD-50186 | biostudies-arrayexpress

Expression data from Saccharomyces cerevisae strains overexpressing RNA-binding hnRNP Yra1

Project description:Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with an imbalance proportion of Yra1, a component of THO/TREX. We used microarrays to the global impact of Yra1 overexpression and found that no general impact was observed. S. cerevisiae strains were grown in minimal medium raffinose and were shifted to galactose (2%) for four hours in liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays

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Expression data from Saccharomyces cerevisiae strains deleted for the THSC/TREX-2 subunits Thp1, Sac3 and Sus1

2014-10-08 | GSE56702 | GEO

Expression data from Saccharomyces cerevisiae strains deleted for different subunits of the THO/TREX complex

2011-06-29 | GSE24802 | GEO

Expression data from Saccharomyces cerevisae strains deleted for the RNA-binding hnRNP Npl3

Project description:Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with a suboptimal assembly of the nascent messenger ribonucleo-protein particle (mRNP), as THO/TREX and some heterogeneous nuclear ribonucleoproteins (hnRNPs) mutants. We used microarrays to the global impact of Npl3 in gene expression and found that Npl3 deletion has a functional impact in highly-expressed, long and G+C rich genes regardless of gene function

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Expression data from Saccharomyces cerevisae RNAPII mutant strains

Project description:Transcription is a major contributor to genome instability. A main cause of transcription-associated instability relies on the capacity of transcription to stall replication. Such genome instability is increased in RNAPII mutants. We performed microarrays to analyze the effect of RNAPII mutations on gene expression. The results indicate there is neither a common profile of gene expression nor genes whose gene expression alterations could reasonably explain the genome instability phenotypes of the RNAPII mutants. S. cerevisiae strains were grown in YPD liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays

2014-12-04 | E-GEOD-55223 | biostudies-arrayexpress

Expression data from Saccharomyces cerevisiae strains carrying the rna14-1 or the rna15-1 allele

Project description:In the yeast Saccharomyces cerevisiae, cleavage factor I (CFI) and cleavage and polyadenylation factor (CPF) build the core of the transcription termination machinery. CFI comprises the Rna14, Rna15, Pcf11, and Clp1 proteins, as well as the associated Hrp5 RNA-binding protein. We found that CFI participates in the DNA damage response and that rna14-1 shows synthetic growth defects with mutants of different repair pathways, including homologous recombination, non-homologous end joining, post replicative repair, mismatch repair, and nucleotide excision repair, implicating that impaired RNAPII termination and 3â-end processing decreases the cellular tolerance for DNA damage. Beyond replication progression defects, we found that bypass of the G1/S checkpoint in rna14-1 cells leads to synthetic sickness, accumulation of phosphorylated H2A, as well as increase in Rad52-foci and in recombination. Our data provide evidence that CFI dysfunction impairs RNAPII turnover, leading to replication hindrance and lower tolerance to exogenous DNA damage. These findings underscore the importance of coordination between transcription termination, DNA repair and replication in the maintenance of genomic stability. S. cerevisiae strains were grown in YPAD liquid culture at 30Â°C, total RNA was isolated and hybridized on Affymetrix microarrays.

2014-03-31 | E-GEOD-50947 | biostudies-arrayexpress

Strain differences in copper sulfate

Project description:Each strain was grown overnight then diluted in fresh rich media. After three hours strains were again rediluted into either rich media or rich media supplemented with copper sulfate. After another three hours cultures were sampled, cells lysed and flash frozen using liquid nitrogen. RNA was extrated using hot phenol-chloroform, reverse transcripbed using amino-allyle dUTP and labelled with either Cy3 or Cy5 flourescent dye. Each hybridization is of a single sample compared to a reference pool contructed from all the strains with the same treatment. Labelled probe were hybridized to DNA microarrays spotted with 6144 70 bp oligonucleotides obtained from Qiagen-Operon. After an overnight hybridization, microarrays were scanned using a GenePix 4000A scanner and spot intensities extracted using GenePix 4.0 software. Bad spots were flagged based on the image. Keywords: other

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