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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition

ABSTRACT: Biogenesis of eukaryotic messenger ribonucleoprotein complexes (mRNPs) involves the synthesis, splicing, and 3M-bM-^@M-^Y-processing of pre-mRNA, and the assembly of mature mRNPs for nuclear export. We mapped 23 mRNP biogenesis factors onto the newly synthesized yeast transcriptome, providing ~10^5-10^6 high-confidence RNA interaction sites per factor. PAR-CLIP data of 23 mRNP biogenesis factors in Saccharomyces cerevisiae

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Carlo BM-CM-$jen

PROVIDER: E-GEOD-59676 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition

Project description:Biogenesis of eukaryotic messenger ribonucleoprotein complexes (mRNPs) involves the synthesis, splicing, and 3’-processing of pre-mRNA, and the assembly of mature mRNPs for nuclear export. We mapped 23 mRNP biogenesis factors onto the newly synthesized yeast transcriptome, providing ~10^5-10^6 high-confidence RNA interaction sites per factor.

2014-07-23 | GSE59676 | 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

Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA

Project description:RNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein-RNA and protein-protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate several functions at once and likely impact the structural integrity of the large mRNP assemblies, these proteins often function in. Thus, the function of the RNA-binding activity of RBPs is often unknown. Using UV-induced RNA-protein crosslinking and subsequent mass spectrometric (MS) analysis, we first identified more than 100 in vivo RNA crosslinks in 16 nuclear mRNP components. For functional analysis, we chose Npl3, for which we identified crosslinks in its two RNA recognition motifs (RRMs) as well as in the flexible linker connecting the two. Both RRM domains and the linker uniquely contribute to RNA recognition. Interestingly, mutations in each of these three regions cause different phenotypes, indicating distinct functions of the different RNA-binding domains of Npl3. Notably, the npl3-Linker mutant strongly impairs recruitment of some mRNP components to chromatin and the incorporation of other mRNP components into nuclear mRNPs, establishing a function of Npl3 in mRNP assembly. Taken together, we determined the specific function of the RNA-binding activity of a nuclear mRNP component, an approach that can be applied to many RBPs in any RNA metabolic process.

2023-03-11 | PXD035153 | Pride

Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA

Project description:Assessing the function of the RNA-binding activity of RNA-binding proteins (RBPs) is challenging. Here, Keil et al. use a targeted XL-ms approach to identify RNA-binding sites in components of nuclear mRNPs in S. cerevisiae. The analysis of RNA-binding mutants of one selected example, the SR-like protein Npl3, uncovers two novel functions of Npl3, namely in the recruitment of mRNP components to transcribed protein-coding genes and their transfer onto the mRNA. This data set applies label-free protein quantification to assess protein abundancies in NPL3 or CBC2 affinity purification experiments from cellular lysates of NPL3-WT and NPL3-P196D/A197D double-mutant expressing cells.

2023-03-11 | PXD034656 | Pride

Global Analysis of Yeast mRNPs

Project description:Proteins regulate gene expression by controlling mRNA biogenesis, localization, translation and decay. Identifying the composition, diversity and function of mRNPs (mRNA protein complexes) is essential to understanding these processes. In a global survey of S. cerevisiae mRNA binding proteins we identified 120 proteins that cross-link to mRNA, including 66 new mRNA binding proteins. These include kinases, RNA modification enzymes, metabolic enzymes, and tRNA and rRNA metabolism factors. These proteins show dynamic subcellular localization during stress, including assembly into stress granules and P-bodies (Processing-bodies). CLIP (cross-linking and immunoprecipitation) analyses of the P-body components Pat1, Lsm1, Dhh1 and Sbp1 identified sites of interaction on specific mRNAs revealing positional binding preferences and co-assembly preferences. Taken together, this work defines the major yeast mRNP proteins, reveals widespread changes in their subcellular location during stress, and begins to define assembly rules for P-body mRNPs. CLIP-seq analysis of Dhh1, Lsm1, Pat1 and Sbp1

2013-04-18 | E-GEOD-46142 | biostudies-arrayexpress

Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome (RNA-seq dataset)

Project description:In order to dissect the nuclear RNA quality control (QC) mechanisms, we used a powerful assay based on global perturbation of mRNP biogenesis in yeast Saccharomyces cerevisiae by the bacterial Rho helicase. We have monitored the global RNA levels upon Rho activation and compare it to basal RNA level in WT strain, which have revealed down-regulated transcripts. Then, the same experiment was performed but in a strain lacking Rrp47, giving us a precise overview of the QC targets. We also followed some QC components (Nrd1, Nab3, Trf4 and Rrp6) along the yeast chromosomes by ChIP-seq before and after perturbation of mRNP biogenesis by Rho (crosslinked dataset).

2019-12-04 | E-MTAB-7538 | biostudies-arrayexpress

Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome (ChIP-seq dataset)

Project description:In order to dissect the nuclear RNA quality control (QC) mechanisms, we used a powerful assay based on global perturbation of mRNP biogenesis in yeast Saccharomyces cerevisiae by the bacterial Rho helicase. We have monitored the global RNA levels upon Rho activation and compare it to basal RNA level in WT strain, which have revealed down-regulated transcripts. Then, the same experiment was performed but in a strain lacking Rrp47, giving us a precise overview of the QC targets (crosslinked dataset). We also followed some QC components (Nrd1, Nab3, Trf4 and Rrp6) along the yeast chromosomes by ChIP-seq before (NI) and after (I) perturbation of mRNP biogenesis by Rho.

2019-12-04 | E-MTAB-7539 | biostudies-arrayexpress

Epstein-Barr virus protein EB2 stimulates translation initiation of mRNAs through direct interactions with both PABP and eIF4G

Project description:Epstein-Barr virus (EBV) expresses several mRNAs produced from intronless genes that could be unfavorably translated in front of cellular spliced mRNAs. To overpass these limitations, the virus encodes a RNA-binding protein (RBP), EB2, which is already known to facilitate nuclear mRNAs export and to increase their translational yield. Here we show that EB2 binds both nuclear and cytoplasmic cap-binding complexes (respectively, CBC and eIF4F), and the poly(A)-binding protein (PABP) to enhance translation initiation of a given mRNP. Interestingly, such effect can be obtained only if EB2 was initially bound to the native mRNPs in the nucleus. We also demonstrate that the EB2-eIF4F-PABP association renders the translation of these mRNPs less sensitive to inhibitors of initiation. Taken together, our new data suggest that EB2 binds and stabilizes cap-binding complexes to increase mRNP translation and demonstrate the importance of the mRNP assembly process in the nucleus to promote translation in the cytoplasm.

2022-03-03 | PXD003800 | Pride

Global Analysis of Yeast mRNPs

2013-04-18 | GSE46142 | GEO

RIP-seq analysis of Isw1 interacting transcripts

Project description:This experiment captures the poly(A)RNAs co-immunoprecipated with Isw1 in WT and npl3-1 cells. Chromatin remodelers play an essential role in regulating DNA transaction processes. The yeast chromatin remodeling complex ISW1 displays an unexpected function in nuclear mRNP surveillance, retaining premature mRNPs in proximity to their transcription site. This activity of ISW1 requires its recruitment onto chromatin, its interaction with mRNPs but not its nucleosome sliding activity. In npl3-1 cells, mRNA export is compromised resulting in an increased association of mRNAs with Isw1.

2016-11-17 | E-MTAB-4826 | biostudies-arrayexpress

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