Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA276073 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1813250.fastq.gz | Fastqsanger.gz | |||
| SRR1813251.fastq.gz | Fastqsanger.gz | |||
| SRR1813252.fastq.gz | Fastqsanger.gz | |||
| SRR1813253.fastq.gz | Fastqsanger.gz | |||
| SRR1813254.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: mRNA translation into protein is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants has yet to be systematically studied. Using high-throughput sequencing (RNA-seq), we have measured cellular levels of mRNAs and ncRNAs, and their isoforms, in lymphoblast cell lines (LCL) and in polysomal fractions, the latter shown to yield strong correlations of mRNAs with expressed protein levels. Analysis of allelic RNA ratios at heterozygous SNPs served to reveal genetic factors in ribosomal loading. Methods: RNA-seq was performed on cytosolic extracts and polysomal fractions (3 ribosomes or more) from three lymphoblastoid cell lines. As each RNA fraction was amplified (NuGen kit), and relative contributions from various RNA classes differed between cytosol and polysomes, the fraction of any given RNA species loaded onto polysomes was difficult to quantitate. Therefore, we focused on relative recovery of the various RNA classes and rank order of single RNAs compared to total RNA. Results: RNA-seq of coding and non-coding RNAs (including microRNAs) in three LCLs revealed significant differences in polysomal loading of individual RNAs and isoforms, and between RNA classes. Moreover, correlated distribution between protein-coding and non-coding RNAs suggests possible interactions between them. Allele-selective RNA recruitment revealed strong genetic influence on polysomal loading for multiple RNAs. Allelic effects can be attributed to generation of different RNA isoforms before polysomal loading or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Several variants and genes identified by this approach are also associated with RNA expression and clinical phenotypes in various databases. Conclusions: These results provide a novel approach using complete transcriptome RNA-seq to study polysomal RNA recruitment and regulatory variants affecting protein translation. cells from 3 samples were grown to 5x105 cells/mL density in T75 tissue culture flask and harvested, total RNA and polysome bound RNA was sequenced by Ion Proton
2015-06-30 | E-GEOD-66135 | biostudies-arrayexpress
Project description:Purpose: mRNA translation into protein is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants has yet to be systematically studied. Using high-throughput sequencing (RNA-seq), we have measured cellular levels of mRNAs and ncRNAs, and their isoforms, in lymphoblast cell lines (LCL) and in polysomal fractions, the latter shown to yield strong correlations of mRNAs with expressed protein levels. Analysis of allelic RNA ratios at heterozygous SNPs served to reveal genetic factors in ribosomal loading. Methods: RNA-seq was performed on cytosolic extracts and polysomal fractions (3 ribosomes or more) from three lymphoblastoid cell lines. As each RNA fraction was amplified (NuGen kit), and relative contributions from various RNA classes differed between cytosol and polysomes, the fraction of any given RNA species loaded onto polysomes was difficult to quantitate. Therefore, we focused on relative recovery of the various RNA classes and rank order of single RNAs compared to total RNA. Results: RNA-seq of coding and non-coding RNAs (including microRNAs) in three LCLs revealed significant differences in polysomal loading of individual RNAs and isoforms, and between RNA classes. Moreover, correlated distribution between protein-coding and non-coding RNAs suggests possible interactions between them. Allele-selective RNA recruitment revealed strong genetic influence on polysomal loading for multiple RNAs. Allelic effects can be attributed to generation of different RNA isoforms before polysomal loading or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Several variants and genes identified by this approach are also associated with RNA expression and clinical phenotypes in various databases. Conclusions: These results provide a novel approach using complete transcriptome RNA-seq to study polysomal RNA recruitment and regulatory variants affecting protein translation.
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Project description:Single-cell RNA-sequencing of mouse fibroblasts for the identification and functional characterization of non-coding RNAs. Non-coding RNAs were assigned putative functions based on single-cell expression patters, e.g. phase specific expression during the cell cycle. Additionally, allele-level resolution was used to characterize coordinated and mutually exclusive expressions of noncoding RNAs against nearby protein coding genes.
2018-12-19 | E-MTAB-6385 | biostudies-arrayexpress
Project description:We performed ribosome profiling of polysomes (Poly-RIBOseq) to monitor translation of RNAs associated with polysomes in brain extracts from a mouse model Keywords: ribosome profiling, translation, polysome profiling, Poly-RIBOseq
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Project description:Methyl-7-guanosine (m7G) “capping” of coding and some noncoding RNAs is critical for their maturation and subsequent activity. Here, we discovered that eukaryotic translation initiation factor 4E(eIF4E), itself a cap-binding protein, drives the expression of the capping machinery and the increased capping efficiency of ∼100 coding and noncoding RNAs. This dataset collects transcriptomic data for quantitative cap immunoprecipitation (CapIP) assay in eIF4E-Flag or vector stable U2Os cells.
2020-09-30 | GSE158728 | GEO
Project description:Exon junction complexes (EJCs) deposited on spliced mRNAs play multifunctional roles in the regulation of gene expression. Whereas the formation and components of EJCs are well characterized, the underlying molecular mechanisms for gene regulation remain poorly understood. Here we find that a eukaryotic translation initiation factor (eIF) 4A3, a core component of EJC directly interacts with eIF3g, a subunit of eIF3 complex. This interaction serves as a linker between the EJC and eIF3 complex, consequently driving an internal ribosomal recruitment. Accordingly, artificially tethered EJC component or cellular EJC deposited on mRNA after splicing promotes internal initiation of translation in a way that is resistant to cellular stress induced by serum starvation. We also demonstrate that translatable endogenous or reporter circular RNAs depend on EJC for their association with polysomes. Our results uncover an internal initiation driven by EJC, expanding the protein-coding potential of human transcriptome including circular RNAs.
2023-08-31 | GSE131563 | GEO
Project description:Pervasive translation is a widespread phenomenon that plays an important role in de novo gene birth; however, its underlying mechanisms remain unclear. Based on multiple Ribosome Profiling datasets, we investigated the translational landscape of coding and noncoding regions of yeast. Therefore, we developed a new representation framework which allows the visual and comprehensive representation of the diversity of translation behaviors in yeast coding and noncoding regions. We show that if coding regions are restricted to specific regions of the translation landscape, noncoding regions are associated with a wide diversity of translation behaviors and, in contrast, populate the entire yeast translational landscape. In particular, we reveal that noncoding regions are associated with canonical translation signals but also with novel categories of translation events absent from coding regions, and which seem to be a hallmark of pervasive translation. Notably, we report thousands of translated noncoding ORFs among which, 256 led to detectable products with Mass Spectrometry while being characterized by canonical but also non-canonical translation signals. Finally, we show that the translation behavior of noncoding ORFs is not explained by features related to the emergence of function, but is rather determined by the translation start codon and the codon distribution in the three competing RNA frames. Overall, our results enable us to propose a topology of the pervasive translation landscape of a species, and open the way to future comparative analyses of this translation landscape under different conditions.
2024-09-04 | PXD040766 | Pride
Project description:Interventions: Case series:Nil
Primary outcome(s): intestinal microecological disorders;blood non-coding RNAs and immune status
Study Design: Randomized parallel controlled trial
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Project description:Gemin5-dependent RNA association to polysomes supports selective translation of mRNA subsets
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