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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.

ORGANISM(S): Schizosaccharomyces pombe Saccharomyces cerevisiae

PROVIDER: GSE24802 | GEO | 2011/06/29

SECONDARY ACCESSION(S): PRJNA132295

REPOSITORIES: GEO

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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.

2011-06-28 | E-GEOD-24802 | biostudies-arrayexpress

Genome-wide binding of THO and Sub2 in Saccharomyces cerevisiae

Project description: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 an open question. 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 RNAPII, evenly distributed from promoter to termination regions, THO and Sub2 are absent at promoters and distributed in a sharp 5M-bM-^@M-^YM-bM-^FM-^R3M-bM-^@M-^Y gradient. Importantly, ChIP-chips reveal an over-recruitment of Rrm3 in active genes in THO mutants that is reduced by overexpression of RNase H1. Our work establishes a genome-wide function for THO-Sub2 in transcription elongation and mRNP biogenesis that function to prevent the accumulation of transcription-mediated replication obstacles, including R-loops. ChIP-chip studies were perfomed with tagged forms of the Hpr1 component of THO (Hpr1-FLAG), the Sub2 RNA-dependent ATPase of TREX (Sub2-FLAG), the Rpb3 subunit of RNA polymerase II (Rpb3-PK) and the Rrm3 protein (Rrm3-FLAG) in the yeast S. cerevisiae.

2011-06-28 | E-GEOD-24960 | biostudies-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 | biostudies-arrayexpress

Genome-wide binding of THO and Sub2 in Saccharomyces cerevisiae

Project description: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 an open question. 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 RNAPII, evenly distributed from promoter to termination regions, THO and Sub2 are absent at promoters and distributed in a sharp 5’→3’ gradient. Importantly, ChIP-chips reveal an over-recruitment of Rrm3 in active genes in THO mutants that is reduced by overexpression of RNase H1. Our work establishes a genome-wide function for THO-Sub2 in transcription elongation and mRNP biogenesis that function to prevent the accumulation of transcription-mediated replication obstacles, including R-loops.

2011-06-29 | GSE24960 | GEO

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

2014-10-08 | GSE56702 | GEO

Transcription and export complex (THO/TREX) coordinates transcription termination in Arabidopsis

Project description:Transcription termination of mRNAs transcribed from a given locus has a decisive role in regulating the gene function as it determines the coding potential and inclusion of regulatory sequence elements. Failure in appropriate transcription termination leads to read-through transcription, resulting in the synthesis of antisense RNAs which can have profound impact on overall gene expression. However, molecular mechanisms which regulate transcription termination and chimeric RNA formation are poorly understood. We explored the regulatory function of transcription and export complex (THO/TREX) in transcription termination. We show that two members of THO/TREX complex, TREX COMPONENT 1 (TEX1) and HYPER RECOMBINATION1(HPR1) are critical for the correct transcription termination in Arabidopsis. We first demonstrate this by showing defective termination of the bacterial nopaline synthase (NOS) terminator on a transgene in tex1 and hpr1 mutants. Additionally, we show that RNA termination defects in tex1 and hpr1 mutants are widespread at the whole genome levels leading to 3’UTR extensions, truncations and in some cases in the formation of intergenic chimeric transcripts. Chromatin immunoprecipitation coupled with quantitative PCR experiments confirmed the presence of RNA polymerase II beyond the canonical termination sites on genes with defective RNA termination in tex1 and hpr1 mutants. These results demonstrate that THO/TREX complex is a novel regulator of transcription termination in Arabidopsis.

2020-03-24 | GSE128877 | GEO

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 | biostudies-arrayexpress

Transcription and export complex (THO/TREX) coordinates transcription termination in Arabidopsis

Project description:Transcription and export complex (THO/TREX) coordinates transcription termination in Arabidopsis

| PRJNA529202 | ENA

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

2013-01-31 | GSE27091 | 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. 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

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