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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Nuclear mRNA quality control is bypassed for rapid export of stress responsive transcripts (Microarray)

ABSTRACT: Comparative analyses of Mex67 and Npl3 binding to mRNA at normal growth condition (25Â°C) and upon shift to heat stress (30 min, 42Â°C). Comparative analyses of mRNA binding of Mex67, Npl3 and no tag control at normal growth condition (25Â°C) and upon heat stress (30 min, 42Â°C) via RNA Co-IP experiments. Respective co-purified mRNAs were subjected to cDNA Microarray chips.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Gabriela Salinas-Riester

PROVIDER: E-GEOD-83267 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Nuclear mRNA quality control is bypassed for rapid export of stress responsive transcripts [RNA-Seq]

Project description:Comparative analyses of Mex67 and Npl3 binding to mRNA at normal growth condition (25°C) and upon shift to heat stress (30 min, 42°C).

2016-12-13 | GSE81542 | GEO

Nuclear mRNA quality control is bypassed for rapid export of stress responsive transcripts (Microarray)

Project description:Comparative analyses of Mex67 and Npl3 binding to mRNA at normal growth condition (25°C) and upon shift to heat stress (30 min, 42°C).

2016-06-14 | GSE83267 | GEO

Quality control of spliced mRNAs requires the shuttling SR-proteins Gbp2 and Hrb1

Project description:Eukaryotic cells have to prevent the export of unspliced pre-mRNAs until intron removal is completed to avoid the expression of aberrant and potentially harmful proteins. Only mature RNAs associate with the export receptor Mex67 (mammalian TAP) and enter the cytoplasm. The underlying nuclear quality control mechanisms are still unclear. Here we show that two shuttling SR-proteins Gbp2 and Hrb1 are key surveillance factors for the selective export of spliced mRNAs in yeast. Their absence leads to the significant leakage of unspliced pre-mRNAs into the cytoplasm. They bind to pre-mRNAs and the spliceosome during splicing, where they are necessary for the surveillance of splicing and the stable binding of the TRAMP-complex to the spliceosome-bound transcripts. Faulty transcripts are marked for their degradation at the nuclear exosome. On correct mRNAs the SR-proteins recruit Mex67 upon completion of splicing to allow a quality controlled nuclear export. Altogether, these data identify a role for shuttling SR-proteins in mRNA surveillance and nuclear mRNA quality control. 6 samples, i.e. 2 replicates per protein Gbp2, Hrb1 and Npl3

2013-12-04 | E-GEOD-52808 | biostudies-arrayexpress

The shuttling SR-like proteins Gbp2 and Hrb1 mediate the nuclear export of spliced mRNAs

Project description:Three shuttling SR-like proteins exist in Saccharomyces cerevisiae, Npl3, Gbp2 and Hrb1, that are involved in the nuclear export of mRNAs. In a screen for genes that regulate the export of Gbp2, we identified novel mutants of the splicing factors PRP8 and PRP17 that lead to severe mislocalization defects for Gbp2 and Hrb1, but not Npl3. Microarray and qRT-PCR analyses show that Gbp2 and Hrb1 preferentially bind to transcripts derived from intron-containing genes. Moreover, in contrast to Npl3, Gbp2 and Hrb1 show genetic and physical interactions with late splicing factors such as Prp17 and Prp43. Further, RNA co-immunoprecipitation experiments reveal that, unlike Npl3, association of Gbp2 and Hrb1 with the mRNA requires splicing, and this in turn is required for their Mex67 recruitment. We propose a model in which Gbp2 and Hrb1 are attached to the mRNAs at late stages of splicing to promote the subsequent export of spliced mRNAs. keyword: RIP-chip RNA-IP of endogenously expressed 3-fold C-terminal myc-tagged Gbp2 and Hrb1 in S288C background cells was each performed once in cells grown to a density of 4x10^7 cells/ml and hybridized against a total (input) RNA reference.

2013-08-30 | E-GEOD-20738 | biostudies-arrayexpress

Identification of HS-responsive genes in rice

Project description:To characterize plant heat stress-responsive genes and to clarify the heat stress-responsive transcription pathways, the transcriptome analysis of rice was conducted using microarray. Rice (Oryza sativa L. cv. Nipponbare) were grown in plastic pots filled with nutrient soil for 2 weeks with a 12 h light (28Â°C)/12 h dark (25Â°C) regimen (ca. 1500 Î¼mol photons mâ2 sâ1) and were treated for 30 min at 42Â°C.

2017-02-23 | E-MTAB-4503 | biostudies-arrayexpress

Transcription profiling by array of heat-stressed maize plants

Project description:To characterize plant heat stress-responsive genes and to clarify the heat stress-responsive transcription pathways, the transcriptome analysis of maize was conducted using microarray. Maize (Zea mays cv. B73) were grown in plastic pots filled with nutrient soil for 2 weeks with a 12 h light (28Â°C)/12 h dark (25Â°C) regimen (ca. 1500 Î¼mol photons mâ2 sâ1) and were treated for 30 min at 42Â°C.

2017-02-28 | E-MTAB-4530 | biostudies-arrayexpress

Identification of heat stress-responsive genes in soybean

Project description:To characterize heat stress-responsive genes and to clarify the heat stress-responsive transcription pathways, transcriptome analysis of soybean was conducted using microarray. Soybean (Glycine max cv. Williams82) were grown in plastic pots filled with nutrient soil for 2 weeks with a 12 h light (28Â°C)/12 h dark (25Â°C) regimen (ca. 1500 Î¼mol photons mâ2 sâ1) and were treated for 30 min at 42Â°C.

2017-02-23 | E-MTAB-4504 | biostudies-arrayexpress

The SR-like protein Npl3 transfers mRNP components from the transcription site onto the mRNA

Project description:In order to determine specifically the RNA-binding function of proteins involved in nuclear mRNP assembly, we first determined the amino acids involved in RNA-binding by RNPXL. We identified about 100 amino acids cross-linked to RNA in vivo in the nuclear mRNP components Npl3, Nab2, Tho1, Mex67-Mtr2 and the TREX complex. Second, we can now specifically elucidate the function of the RNA-binding activity of these proteins by mutation of the identified amino acids. Npl3 is an SR-like protein with functions in transcription elongation, splicing, 3’ end processing, mRNP assembly and nuclear mRNA export. The middle part of Npl3 consists of two RNA recognition motif (RRM) domains, RRM1 and RRM2, connected by an eight amino acid long flexible linker. In order to analyze the function of the RNA-binding activity of Npl3, we mutated several amino acids that cross-linked to RNA. We generated three npl3 mutants, one in the RRM1, one in the linker and a third in the RRM2 domain, and elucidated the functional consequences of these mutations. Interestingly, these three npl3 mutants show different phenotypes. Thus, abrogation of mRNA-binding in different regions of Npl3 has different functional outcomes. Furthermore, analysis of the npl3-Linker mutant revealed a novel function of Npl3. Npl3 functions in the transfer of nuclear mRNP components from the site of transcription onto the mRNA. Taken together, we identify the in vivo RNA-binding sites of nuclear mRNA-binding proteins involved in mRNP assembly and nuclear mRNA export. In addition, we show that abrogation of RNA-binding in different regions of the protein Npl3 has specific and surprisingly different functional consequences. Furthermore, we uncovered a novel function of Npl3 in nuclear mRNP assembly.

2022-11-26 | GSE160709 | GEO

ChIP-chip data of Npl3-Myc and Rrm3-Flag in wild-type and npl3M-bM-^HM-^F cells

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. Here we show that yeast npl3M-bM-^HM-^F cells show genome-wide replication obstacles as determined by accumulation of the Rrm3 helicase. Such obstacles preferentially occur at long and highly expressed genes, to which Npl3 is preferentially bound in wild-type cells. ChIP-chip studies were perfomed with antibodies against Myc-tagged Npl3 protein in wild-type cells of the yeast S. Cerevisiae, as well as Flag-tagged Rrm3 protein in both wild-type and npl3M-bM-^HM-^F cells.

2013-11-15 | E-GEOD-50185 | biostudies-arrayexpress

Transcription profiling of Drosophila melanogaster third instar larvae organ cultures treated with 20-hydroxyecdysone, cycloheximide vs controlds to identify 20-hydroxyecdysone regulated genes at the onset of metamorphosis

Project description:To identify 20E-regulated genes, wandering third instar larvae were dissected and their organs were cultured in the presence of either no hormone, 20E alone, cycloheximide alone, or 20E plus cycloheximide for six hours. Experiment Overall Design: Eight partial blue gut third instar larvae were dissected in each well of a 9 well glass dish (Corning) and cultured in ~100 Âµl oxygenated Schneiders Drosophila Medium (Gibco) at 25Â°C. Cultures were incubated in an a styrofoam box under a constant flow of oxygen. Following an initial incubation of 1 hour, the medium was removed and replaced with either fresh Schneiders Drosophila Medium (no hormone), medium plus 8.5x10-5 M cycloheximide (Sigma), medium plus 5x10-6 M 20-hydroxyecdysone (Sigma), or medium plus cycloheximide and 20E, each for 6 hrs at 25Â°C. Organs were collected and RNA extracted from these samples was analyzed on Affymetrix Drosophila Genome Arrays.

2007-10-31 | E-GEOD-3060 | biostudies-arrayexpress

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