Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA109405 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR014368.fastq.gz | Fastqsanger.gz | |||
| SRR014369.fastq.gz | Fastqsanger.gz | |||
| SRR014370.fastq.gz | Fastqsanger.gz | |||
| SRR014371.fastq.gz | Fastqsanger.gz | |||
| SRR014372.fastq.gz | Fastqsanger.gz |
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Project description:We developed a high throughput 5’P sequencing approach (HT-5PSeq) to investigate 5'P mRNA degradome in relation with translation process. This approach is easy and scalable; and uses an affordable rRNA depletion based on duplex-specific nuclease treatment. We use it to investigate in vivo ribosome stalls in S. cerevisiae and S. pombe at single nucleotide resolution. We investigate the 5’P degradation profiles associated to ribosome pausing, its regulation in stress conditions and the relative poly(A) length of mRNA degradation intermediates.
2021-04-02 | GSE152375 | GEO
Project description:The ribosome associated complex (RAC) is a ribosome bound protein chaperone complex reported to surveil the translation of proteins with positively charged regions. It has been posited that RAC might be able to directly regulate translation by coupling co-translational folding with the peptide-elongation cycle. To identify the targets of RAC in cells and test the hypothesis that the complex modulates translation, we performed ribosome profiling on wild- type yeast cells and cells lacking a key component of the RAC that binds near the ribosome active site (zuo1Δ). Ribosome profiling is a sequencing-based technique that allows us to take a nucleotide resolution snapshot of where every ribosome sits on every mRNA in a cell at a given point in time. This powerful approach can provide information about the contributions of individual proteins to the translational landscape of a cell. We identified >300 targets for the RAC, and unexpectedly observed that the ribosome frameshifts on ~10% of these targets in zuo1Δ cells. The maintenance of ribosome reading frame is essential for cell health because frameshifts can result in the production of non-functional truncated and extended protein products. These studies have the potential to uncover RAC as a critical determinant of translational fidelity in eukaryotic cells.
2023-06-01 | GSE151370 | GEO
Project description:Translation Inhibitors Cause Abnormalities in Ribosome Profiling Experiments
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Project description:High-resolution view of the yeast meiotic program revealed by ribosome profiling
| PRJNA149975 | ENA
Project description:We developed RiboLace, a novel method based on a new puromycin-containing molecule, for the isolation of active ribosomes by means of an antibody-free and tag-free pull-down approach. RiboLace is fast, it works with very low input material and can be easily and rapidly used to enhance Ribo-Seq, obtaining a global snapshot on active ribosome footprints at single nucleotide resolution from eukaryotic in vitro and in vivo systems. Keywords: ribosome profiling, translation, RiboLace, Ribo-Seq, active translation
2018-10-09 | GSE102354 | GEO
Project description:We developed RiboLace, a novel method based on a new puromycin-containing molecule, for the isolation of active ribosomes by means of an antibody-free and tag-free pull-down approach. RiboLace is fast, it works with very low input material and can be easily and rapidly used to enhance Ribo-Seq, obtaining a global snapshot on active ribosome footprints at single nucleotide resolution from eukaryotic in vitro and in vivo systems. Keywords: ribosome profiling, translation, RiboLace, Ribo-Seq, active translation
2018-10-09 | GSE112353 | GEO
Project description:Translation of mRNA into a polypeptide is terminated when the release factor eRF1 recognizes a UAA, UAG, or UGA stop codon in the ribosomal A site and stimulates nascent peptide release. However, stop codon readthrough can occur when a near-cognate tRNA outcompetes eRF1 in decoding the stop codon, resulting in the continuation of the elongation phase of protein synthesis. At the end of a conventional mRNA coding region readthrough allows translation into the mRNA 3’-UTR. Previous studies with reporter systems have shown that the efficiency of termination or readthrough is modulated by cis-acting elements other than stop codon identity, including two nucleotides 5’ of the stop codon, six nucleotides 3’ of the stop codon in the ribosomal mRNA channel, and stem-loop structures in the mRNA 3’-UTR. It is unknown whether these elements are important at a genome-wide level and whether other mRNA features proximal to the stop codon significantly affect termination and readthrough efficiencies in vivo. Accordingly, we carried out ribosome profiling analyses of yeast cells expressing wild-type or temperature-sensitive eRF1 and developed bioinformatics strategies to calculate readthrough efficiency, and to identify mRNA and peptide features which influence that efficiency. We found that the stop codon (nt +1 to +3), the nucleotide after it (nt +4), the codon in the P site (nt -3 to -1), and 3’-UTR length are the most influential features in the control of readthrough efficiency, while nts +5 to +9 and mRNA secondary structure in the 3’-UTR had milder effects. Additionally, we found low readthrough genes to have shorter 3’-UTRs compared to high readthrough genes in cells with thermally inactivated eRF1, while this trend was reversed in wild-type cells. Together, our results demonstrated the general roles of known regulatory elements in genome-wide regulation and identified several new mRNA or peptide features important for translation termination and readthrough.
2020-12-08 | GSE162780 | GEO
Project description:Dynamics of ribosome scanning and recycling revealed by translation complex profiling
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Project description:Ribosome profiling (Ribo-Seq) and RNA-Seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation to determine effects on translation.
2021-09-30 | E-MTAB-9094 | biostudies-arrayexpress
Project description:Protein synthesis by ribosomes takes place on a linear substrate but at variable speeds. Transient pausing of ribosomes can impact a variety of co-translational processes, including protein targeting and folding. These pauses are influenced by the sequence of the mRNA. Thus redundancy in the genetic code allows the same protein to be translated at different rates. However, our knowledge of both the position and the mechanism of translational pausing in vivo is highly limited. Here we present a genome-wide analysis of translational pausing in bacteria using ribosome profiling-deep sequencing of ribosome-protected mRNA fragments. This approach enables high-resolution measurement of ribosome density profiles along most transcripts at unperturbed, endogenous expression levels. Unexpectedly, we found that codons decoded by rare tRNAs do not lead to slow translation under nutrient-rich conditions. Instead, Shine-Dalgarno-(SD) like features within coding sequences cause pervasive translational pausing. Using an orthogonal ribosome possessing an altered anti-SD sequence, we demonstrated that pausing is due to hybridization between mRNA and the 16S rRNA of the translating ribosome. In protein coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites. Our results indicate that internal SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes. Identification of translation pause sites in vivo using ribosome profiling
2012-04-01 | E-GEOD-35641 | biostudies-arrayexpress