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Saccharomyces cerevisiae

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

PROVIDER: PRJNA279885 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1946710.fastq.gz	Fastqsanger.gz
	SRR1946711.fastq.gz	Fastqsanger.gz
	SRR1946712.fastq.gz	Fastqsanger.gz
	SRR1946713.fastq.gz	Fastqsanger.gz
	SRR1946714.fastq.gz	Fastqsanger.gz

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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

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

2015-08-27 | GSE67431 | GEO

Expression data from Saccharomyces cerevisiae strains deleted for the nucleoporin Nup84

Project description:the nuclear pore complex (NPC) is emerging as an important mediator of cellular processes beyond molecule transport, including control of gene expression, replication and DNA repair. We used microarrays to study the global impact of Nup84 in gene expression, in particular expression of DNA repair genes.

2019-01-25 | GSE113118 | GEO

The role of Mediator and Little Elongation Complex in transcription termination

Project description:Mediator is a coregulatory complex involved in regulating the transcription of Pol II-dependent genes. Metazoan Mediator subunit MED26 functions as a docking site for the ELL/EAF-containing Super Elongation Complex (SEC) and L ittle Elongation Complex (LEC), which regulate the expression of distinct genes. MED26 helps to recruit SEC to protein-coding genes including c-Myc and LEC to small nuclear RNA (snRNA) genes. However, why MED26 takes advantage of SEC or LEC to regulate different claases of genes is unclear. Here, we present evidence that MED26 recruits LEC to support optimal transcription termination at non-polyadenylated genes including snRNA and replication-dependent histone (RDH) genes. Our findings indicate that LEC recruited by MED26 promotes efficient transcription termination by Pol II through interaction with CBC-ARS2 and NELF/DSIF, and then LEC promotes 3’-end processing through the recruitment of Integrator or Heat labile factor to snRNA or RDH genes, respectively.

2020-01-21 | GSE121024 | 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. 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

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

2011-06-29 | GSE24802 | GEO

Linking Key Steps of MicroRNA Biogenesis by TREX-2 and the Nuclear Pore Complex in Arabidopsis

Project description:Linking Key Steps of MicroRNA Biogenesis by TREX-2 and the Nuclear Pore Complex in Arabidopsis

| PRJNA632504 | ENA

The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies

Project description:The non-polyadenylated mRNAs of replication-dependent histones (RDHs) and small nuclear RNAs (snRNAs) are synthesized by RNA polymerase II at histone locus bodies (HLBs) and Cajal bodies (CBs), respectively. We previously showed that MED26-containing Mediator regulates the 3'-end processing of non-polyadenylated transcripts by recruiting Little Elongation Complex (LEC) to the genes. HLBs frequently associate with CBs, in which 3'-end processing factors for RDH genes are enriched; however, this association’s role has not been elucidated. Here, we show that disruption of the Mediator docking site for LEC by mutating the MED26-binding site of EAF1, a subunit of LEC, interferes with CBs’ association with HLBs, resulting in decreased inter-chromosome interaction between RDH gene clusters and increased aberrant unprocessed RDH gene transcripts. Our findings suggest a model in which LEC recruitment by Mediator plays a role in CBs’ association with HLBs to facilitate the 3'-end processing of RDH genes by supplying 3'-end processing factors.

2022-04-26 | GSE164144 | GEO

Linking Key Steps of MicroRNA Biogenesis by TREX-2 and the Nuclear Pore Complex in Arabidopsis [miRNA-Seq]

Project description:Linking Key Steps of MicroRNA Biogenesis by TREX-2 and the Nuclear Pore Complex in Arabidopsis [miRNA-Seq]

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Linking Key Steps of MicroRNA Biogenesis by TREX-2 and the Nuclear Pore Complex in Arabidopsis [mRNA-Seq]

Project description:Linking Key Steps of MicroRNA Biogenesis by TREX-2 and the Nuclear Pore Complex in Arabidopsis [mRNA-Seq]

| PRJNA632509 | ENA