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Expression data in HeLa S3 cells transfected with control-, UAP56- or URH49-siRNA

ABSTRACT: Nuclear export of mRNA is an essential process for eukaryotic gene expression. TREX complex couples the gene expression from transcription and splicing to mRNA export. Sub2, a core component of TREX complex in yeast is diversified to two closely related RNA helicases, UAP56 and URH49 in human.UAP56 and URH49 are required for bulk poly (A)+ RNA export but their target genes are quite different. In conclusion, UAP56 and URH49 have a different function in vivo despite the highly similarity. Cytoplasmic RNA was prepared in HeLa cells transfected with control-, UAP56- and URH49-siRNA and analyzed by gene expression array.

ORGANISM(S): Homo sapiens

SUBMITTER: Seiji Masuda

PROVIDER: E-GEOD-18173 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data in HeLa S3 cells transfected with control-, UAP56- or URH49-siRNA

Project description:Nuclear export of mRNA is an essential process for eukaryotic gene expression. TREX complex couples the gene expression from transcription and splicing to mRNA export. Sub2, a core component of TREX complex in yeast is diversified to two closely related RNA helicases, UAP56 and URH49 in human.UAP56 and URH49 are required for bulk poly (A)+ RNA export but their target genes are quite different. In conclusion, UAP56 and URH49 have a different function in vivo despite the highly similarity.

2010-08-15 | GSE18173 | GEO

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.

2011-06-29 | GSE24802 | GEO

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

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

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

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

The m 6 A-methylase complex recruits TREX and regulates mRNA export.

Project description:N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNA. This modification has previously been shown to alter the export kinetics for mRNAs though the molecular details surrounding this phenomenon remain poorly understood. Here we show that the m6A complex (WTAP, KIAA1429, METTL3/14) drives recruitment of the TREX mRNA export complex onto m6A modified mRNAs and this process is essential for the efficient export of certain mRNAs. Depletion of the core m6A complex leads to loss of TREX from mRNAs which undergo the m6A modification. We show that TREX stimulates recruitment of the m6A reader protein YTHDC1 to the mRNP and the m6A complex influences the interaction of TREX with YTHDC1. We suggest that m6A acts as a surrogate for other TREX recruitment mechanisms such as splicing and 5’ capping, in long internal and final exons which may otherwise be devoid of this essential complex for mRNA export.

2018-10-03 | GSE111878 | GEO

Identification and function of components from a divergent mRNA export pathway in trypanosomes

Project description:mRNA export is central to gene regulation and expression. In trypanosomes, transcription is polycistronic, all mRNAs are processed by trans-splicing and export is mediated by non-canonical mechanisms. We have described several conserved mRNA export pathway components in Trypanosoma cruzi, including orthologs of Sub2, a component of the TREX complex, and eIF4AIII, a core component of the exon junction complex (EJC). Few orthologs of proteins involved in mRNA export in higher eukaryotes are detectable in trypanosome genomes and examples of mechanistic divergence well known. To uncover additional components of the trypanosome mRNA maturation and export system we undertook an unbiased search for protein interactors of TcSub2 and TceIF4AIII. Significant overlap between TcSub2 and TceIF4AIII interacting protein cohorts suggests that both proteins associate with similar machinery. We confirmed several interactions with conserved core components of the EJC and multiple additional complexes, together with identification of proteins specific to trypanosomatids. The highly interactive super-interactome uncovered here, capable of supporting RNA processing from splicing through to nuclear export and cytoplasmic events, highlights kinetoplastid-specific and conserved components creating an amalgam to support the unique mRNA maturation mechanisms in trypanosomes.

2022-02-07 | PXD028072 | Pride

TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome

Project description:THOC6 is the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 is critical for mammalian Transcription Export complex (TREX) tetramer formation, which is composed of four six-subunit THO monomers. The TREX tetramer facilitates mammalian RNA processing, in addition to the nuclear mRNA export functions of the TREX dimer conserved through yeast. Human and mouse TIDS model systems revealed novel THOC6-dependent, species-specific TREX tetramer functions. Germline biallelic Thoc6 loss-of-function (LOF) variants result in mouse embryonic lethality. Biallelic THOC6 LOF variants do not alter the expression of TREX dimer component proteins in human cells, but reduced binding affinity to ALYREF implicates impaired TREX tetramer formation. Defects in RNA nuclear export functions were not detected in biallelic THOC6 LOF human neural cells. Instead, mis-splicing was detected in human and mouse neural tissue, revealing novel THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for regulation of key signaling pathways in human corticogenesis that dictate the transition from proliferative to neurogenic divisions, developmental biology implicated in TIDS neuropathology.

2023-10-17 | GSE245121 | GEO

The nuclear pore-associated TREX-2 complex employs the Mediator Med31 submodule as a docking site to regulate gene expression

Project description:Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription and mRNA export. How TREX-2 regulates the gene expression machinery is unknown. Here, we show that TREX-2 interacts with the Mediator complex, an essential regulator of RNA Polymerase (Pol) II. Structural and biochemical studies identify a conserved region on TREX-2, which directly binds the Mediator Med31/Med7N submodule. TREX-2 regulates assembly of Mediator with its Cdk8 kinase and is required for recruitment and site-specific phosphorylation of Pol II. Transcriptome and phenotypic profiling confirm that TREX-2 and Med31 are functionally interdependent. TREX-2 additionally uses its Mediator-interacting surface to regulate mRNA export suggesting a mechanism for coupling transcription initiation and early steps of mRNA processing at the Mediator level. In sum, we provide insight into how NPC-associated adaptor complexes can access the core transcription machinery. RNAseq was performed from WT, sac3∆, cdk8∆ and Sac3 R288D mutant cells. For each strain triplicates were analyzed. WT strain was sac3∆ transformed with pRS315 SAC3 WT

2015-08-27 | E-GEOD-67431 | 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

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