Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of four yeast strains grown in SC medium and shifted for 2.5h to 37C: YRA1 wild type, YRA1 mlp2916; GFP-yra1-8, and GFP-yra1-8 mlp2916

ABSTRACT: Comparison of mRNA levels in four yeast strains grown in SC medium and shifted for 2.5h to 37C: YRA1 wild-type, YRA1 mlp2Δ GFP-yra1-8, and GFP-yra1-8 mlp2Δ

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Francoise Stutz

PROVIDER: E-MEXP-130 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Perinuclear Mlp proteins downregulate gene expression in response to a defect in mRNA export.

Vinciguerra Patrizia P Iglesias Nahid N Camblong Jurgi J Zenklusen Daniel D Stutz Françoise F

The EMBO journal 20050203 4

The mRNA export adaptor Yra1p/REF contributes to nascent mRNP assembly and recruitment of the export receptor Mex67p. yra1 mutants exhibit mRNA export defects and a decrease in LacZ reporter and certain endogenous transcripts. The loss of Mlp1p/Mlp2p, two TPR-like proteins attached to nuclear pores, rescues LacZ mRNA levels and increases their appearance in the cytoplasm, without restoring bulk poly(A)+ RNA export. Chromatin immunoprecipitation, FISH and pulse-chase experiments indicate that Mlp ...[more]

PMID: 15692572

Similar Datasets

total RNA from yra1-1 at 37C vs. Yra1 WT at 37C (yra1-1TS_v_Yra1WT)

Project description:Comparison of cDNA from RNA of yra1-1 temperature-sensitive mutant to RNA from Yra1 wildtype strain both at the non-permissive temperature of 37C Keywords: repeat sample

2002-11-25 | GSE104 | GEO

RNA-seq of Yra1 associated mRNAs

Project description:Gene expression results from mRNA - RNA-binding protein (RBP) interactions within messenger ribonucleoprotein (mRNP) particles. We identified heterogeniety of nuclear mRNP composition involved in mRNA biogenesis and export with different occupancy and stoichiometry of RNA-binding proteins. Especially, mRNA export adopter protein Yra1 showed large variation of its stoichiometry on single mRNPs. We identified stoichiometry of Yra1 in the nuclear cap binding complex (Cbp80) bound mRNPs and it can be dissected into two categories (one and multiple Yra1 bound mRNPs). Multiple Yra1 containing mRNPs specifically co-occupied with THO complex (Hpr1). To investigate gene dependency to form different Yra1 stoichiometry mRNPs, we performed RNA-IP experiment for Yra1 with two step purification by Cbp80/Yra1 and Hpr1/Yra1.

2024-02-14 | GSE226972 | GEO

total RNA from yra1-1 at 37C vs. Yra1 WT at 37C (yra1-1TS_v_Yra1WT)

Project description:Comparison of cDNA from RNA of yra1-1 temperature-sensitive mutant to RNA from Yra1 wildtype strain both at the non-permissive temperature of 37C

2010-05-27 | E-GEOD-104 | biostudies-arrayexpress

ChIP-chip data of HA-Yra1 and Rrm3-Flag in wild-type and cells overexpressing YRA1

Project description:Transcription is a major obstacle for replication fork progression and a cause of genome instability. Yra1 is an essential nuclear factor of the evolutionarily conserved family of hnRNP-like export factors that when overexpressed impairs mRNA export and cell growth. Through this ChIP-chip analysis it is shown that Yra1 binds to active chromatin and is enriched at telomeres when it is overexpressed, in agreement with a possible role of this mRNP factor in the maintenance of telomere integrity. Our data indicate that YRA1 overexpression correlates with replication impairment as inferred by the increase of Rrm3, a helicase involved in the replication fork progression, at transcribed genes and telomeres.

2016-03-11 | GSE68486 | GEO

ChIP-chip data of HA-Yra1 and Rrm3-Flag in wild-type and cells overexpressing YRA1

2016-03-11 | E-GEOD-68486 | biostudies-arrayexpress

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

2016-03-11 | GSE68487 | GEO

Yra1-bound R loops cause orientation-independent transcription-replication collisions and telomere instability

Project description:R loops are an important source of genome instability largely due to its negative impact on replication progression. Yra1/ALY is an abundant RNA-binding factor conserved from yeast to humans and required for mRNA export, but its excess cause lethality and genome instability. Here, we show that Yra1 binds RNA-DNA hybrids in vitro and when artificially overexpressed is recruited to chromatin in an RNA-DNA hybrid-dependent manner stabilizing R loops and converting them into replication obstacles in vivo. Importantly, excess of Yra1 increases R loop-mediated genome instability caused by transcription-replication collisions regardless of whether they are co-directional or head-on. It also induces telomere shortening and senescence, consistent with a defect in telomere replication. Our results indicate that R loops form transiently in cells regardless of replication and, after stabilization by excess Yra1, they compromise genome integrity, in agreement with a two-step model of R loop-mediated genome instability. This work opens new perspectives to understand transcription-associated genome instability in repair-deficient cells, including tumoral cells.

2018-06-27 | GSE113580 | GEO

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 | biostudies-arrayexpress

Transcription profiling of yeast TOP1 null strain bearing plasmids that express wild-type yeast Top1p or an inactive Y727F mutant enzyme and treated with camptothecin

Project description:To establish the effect of CPT in the regulation of global transcription in S. cerevisiae, we have used a yeast TOP1 null strain, JEL1Δtop1, bearing a low-copy number plasmid that expresses, under the control of the yeast TOP1 promoter, either a wild-type (wt) yeast Top1p (pCC10) or an inactive Y727F mutant enzyme (pAR7).We determined global transcript levels upon CPT treatments of JEL1Δtop1 cells expressing either a yeast wt or Y727F mutant Top1p.

2008-06-01 | E-MEXP-1104 | biostudies-arrayexpress

Budding yeast mRNA export and processing factor localization

Project description:The yeast mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A linking export to 3'-end formation. We found a surprising consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit, Clp1, for binding to Pcf11, and excess Yra1 inhibits 3' processing in vitro. Release of Yra1 at the 3' ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit, but instead Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A/B 3' processing factor. Key Words: Yra1, cleavage-polyadenylation, mRNA export, Pcf11, Clp1, Sub2, alternative polyadenylation

2011-09-25 | GSE30705 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

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