Browse
Submit Data
Databases
Help
Login

Dataset Information

7 Views

4 Connections

0 Citations

0 Reanalyses

6 Downloads

Omics score: 2

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

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Andrés Aguilera Antonio Marín Hélène Gaillard Cristina Tous Belén Gómez-González

PROVIDER: E-GEOD-24802 | ArrayExpress | 2011-06-28

SECONDARY ACCESSION(S): GSE24802PRJNA132295

REPOSITORIES: GEO, ArrayExpress

ACCESS DATA

Json Xml

Publications

Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles.

Gómez-González Belén B García-Rubio María M Bermejo Rodrigo R Gaillard Hélène H Shirahige Katsuhiko K Marín Antonio A Foiani Marco M Aguilera Andrés A

The EMBO journal 20110624 15

THO/TREX is a conserved nuclear complex that functions in mRNP biogenesis and prevents transcription-associated recombination. Whether or not it has a ubiquitous role in the genome is unknown. Chromatin immunoprecipitation (ChIP)-chip studies reveal that the Hpr1 component of THO and the Sub2 RNA-dependent ATPase have genome-wide distributions at active ORFs in yeast. In contrast to RNA polymerase II, evenly distributed from promoter to termination regions, THO and Sub2 are absent at promoters a ...[more]

PMID: 21701562

Similar Datasets

Expression profile of HeLa THOC1-depleted stable cell lines (HeTH-4)

Project description:THO/TREX is an eukaryotic conserved complex with a role at the interface between transcription and mRNP biogenesis/export that in yeast has been shown to play an important role in preventing transcription-associated genome instability. However, whereas a role of mammalian THO/TREX in mRNA processing and export seems clear, a role on either transcription or genome stability is still being argued. In this work we show, by microarray analysis of gene expression, that THO depletion in human cell lines has a global effect on transcription, with a significant impact on genes involved in transcription and DNA metabolism. We performed a microarray analysis of gene expression on THOC1-depleted cells in order to know if there was a change in the genome-wide expression profile. Our data data suggest that the absence of THOC1 has a global effect on transcription process Three repeats HeTH-4 and three repeats of HeTH-4 +DOX (THOC1-depleted cells)

2013-01-31 | E-GEOD-27091 | ArrayExpress

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 | 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

2016-03-11 | E-GEOD-68487 | ArrayExpress

Expression profile of ypr045c∆ mutant

Project description:We report a new protein complex with a role in transcription elongation that is formed by Ypr045c (Thp3) and the Csn12 component of the COP9-signalosome. Thp3-Csn12 is recruited to transcribed genes. Their mutations suppress the gene expression defects of mutants of the THO complex involved in mRNP biogenesis and export and show defects in mRNA accumulation. In vivo transcription elongation impairment of thp3∆ mutants is shown by reduction of RNAPII recruitment throughout an active gene and in transcript run on analysis performed in G-less systems. This new complex establishes a novel link between transcription and mRNA processing. Tthree repeats of the wild type control and three of the ypr045c∆ mutant (BY4741 background).

2011-02-23 | E-GEOD-18994 | ArrayExpress

Transcription profiling of yeast nlp3 mutant to study the effect of suboptimal messenger ribonucleo-protein particle assembly on gene expression

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 | ArrayExpress

Expression data from Saccharomyces cerevisiae strains carrying the spt16-11 or the pob3-7 allele

Project description:The conserved FACT (FAcilitates Chromatin Transcription) complex is a chromatin-reorganizing complex that promotes RNAPII transcription through chromatin templates by interacting with histones. It facilitates promoter activation by nucleosome eviction, and transcription elongation by nucleosome disruption and reassembly ahead and behind the RNAP. It also has a role in replication not fully understood yet. Genome-wide microarray analyses in spt16-11 and pob3-7 strains revealed a set of genes whose mRNA levels were altered with respect to the WT levels. These include 48 up-regulated and 80 down-regulated genes that are common to both strains. The up-regulated genes were longer and expressed at lower levels than the genome average whereas the down-regulated genes were more similar to the average of the genome. S. cerevisiae strains were grown in YEPD liquid culture 4 h after a 26-to-30ºC temperature shift, total RNA was isolated and hybridized on Affymetrix microarrays.

2014-03-17 | E-GEOD-54340 | 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 3’-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 30°C, total RNA was isolated and hybridized on Affymetrix microarrays.

2014-03-31 | E-GEOD-50947 | ArrayExpress

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

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

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. Overall design: S. cerevisiae strains were grown in YPAD liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays.

2011-06-29 | GSE24802 | GEO

Expression profile of nab2-1 mutant

Project description:Gene expression in eukaryotes is an essential process that includes transcription, pre-RNA processing and RNA export. All these steps are coupled and normally, any failure in one step affects the other steps and could cause nuclear mRNA retention. One important player in this interface is the poly(A)-RNA binding protein Nab2, which regulates the poly(A)-tail length of mRNAs protecting their 3’-ends from a second round of polyadenylation and facilitating their nucleo-cytoplasmic export. Interestingly, here we show that Nab2 has additional roles in mRNA transcription elongation, tRNA metabolism and rRNA export. We use Genome-wide analysis of expression of nab2-1 mutant to demosntrate that the role of Nab2 in RNAPII transcription and RNAPIII metabolism is not the result of a secondary effect. Our results identify primary targets of nab2 revealing novel functions for Nab2 in transcription and metabolism of most types of RNAs, not only poly(A) mRNAs, indicating that Nab2 function is more ubiquitous than previously anticipated, being a central player in the general and coordinated control of gene expression from transcription elongation to translation initiation. Three repeats of the wild type and nab2-1 mutant

2011-12-01 | E-GEOD-26303 | ArrayExpress

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
GPMDB
JPOST Repository

EGA
EVA
ENA
LINCS
PAXDB

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data