Ontology highlight
ABSTRACT:
PROVIDER: PRJNA675773 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13016600_1.fastq.gz | Fastqsanger.gz | |||
| SRR13016600_2.fastq.gz | Fastqsanger.gz | |||
| SRR13016601_1.fastq.gz | Fastqsanger.gz | |||
| SRR13016601_2.fastq.gz | Fastqsanger.gz | |||
| SRR13016602_1.fastq.gz | Fastqsanger.gz |
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Project description:Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. They also indicate that emergent polypeptides with as few as three basic residues within a 10-residue window tend to slow translation. With the improved mRNA measurements, the variation attributable to translational control in exponentially growing yeast was less than previously reported, and most of this variation could be predicted with a simple model that considered mRNA abundance, upstream open reading frames, cap-proximal structure and nucleotide composition, and lengths of the coding and 5'-untranslated regions. Collectively, our results provide a framework for executing and interpreting ribosome-profiling studies and reveal key features of translational control in yeast. Ribosome-footprint profiling and RNA-seq (total RNA, poly(A) selected, RiboMinus treated, or Ribo-Zero treated) from log-phase S. cerevisiae. The study includes a reanalysis of the two Samples from GSE53313. The reanalyzed data is linked to the Series record.
2016-02-10 | E-GEOD-75897 | biostudies-arrayexpress
Project description:We analyzed the effect of deleting the gene encoding putative RNA helicase DBP1 in budding yeast on translational efficiencies (TEs) genome wide in wild-type or ded1-ts (temperature-sensitive allele of DED1) strains by combining ribosome footprint profiling with RNA-seq analysis of mRNA abundance. This study includes a total of 32 samples comprised of 16 RNA-Seq samples (mRNA) and 16 ribosome footprint profiling samples (ribo). Experiment 1 includes 8 samples, comprised of 4 RNA-Seq samples and 4 ribosome footprint profiling samples, derived from 2 biological replicates each of the dbp1Δ and ded1-ts dbp1Δ mutant strains, cultured in synthetic complete (SC) medium, following shifts in growth temperature from 30°C to 37°C for 2h. Experiment 2 examines the effect of overexpression of DBP1 in rescuing genome-wide translational defects of a ded1-cs mutant (cold-sensitive allele of DED1) and includes 12 samples, 6 RNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates each of WT DED1 (dubbed DED1-CS), ded1-cs and ded1-cs overexpressing DBP1 (ded1-cs_hcDBP1) strains, cultured in SC-Leu-His medium, following shifts in growth temperature from 30°C to 15°C for 10 min. Experiment 3 examines rescue of translational defects of ded1-ts by DBP1 overexpression and includes 12 samples, 6 RNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates each of WT DED1(DED1-TS), ded1-ts and ded1-ts overexpressing DBP1 (ded1-ts_hcDBP1) strains, cultured in SC-Leu-His medium, following shifts in growth temperature from 30°C to 37°C for 2h.
2018-03-01 | GSE111255 | GEO
Project description:Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We focus on multiple myeloma cells exposed to bortezomib, a first-line chemotherapy and proteasome inhibitor. In the absence of drug effects, we found that direct measurement of protein synthesis by pSILAC correlated well with indirect measurement of synthesis from ribosome footprint density. This correlation, however, broke down under bortezomib-induced stress. By developing a statistical model integrating longitudinal proteomic and mRNA-seq measurements, we found that proteomics could directly detect global alterations in translational rate caused by bortezomib; these changes are not detectable by ribosomal profiling alone. Further, by incorporating pSILAC data into a gene expression model, we predict cell-stress specific proteome remodeling events. These results demonstrate that pSILAC provides an important complement to ribosome profiling in measuring proteome dynamics. Timecourse experiment with six points over 48hr after bortezomib exposure in MM.1S myeloma cells. mRNA-seq and ribosome profiling data at each time point.
2017-05-18 | E-GEOD-69047 | biostudies-arrayexpress
Project description:Nuclease-mediated depletion biases in ribosome footprint profiling libraries
| PRJNA613736 | ENA
Project description:During translation elongation, the ribosome ratchets along its mRNA template, incorporating each new amino acid and translocating from one codon to the next. The elongation cycle requires dramatic structural rearrangements of the ribosome. We show here that deep sequencing of ribosome-protected mRNA fragments reveals not only the position of each ribosome but also, unexpectedly, its particular stage of the elongation cycle. Sequencing reveals two distinct populations of ribosome footprints, 28-30 nucleotides and 20-22 nucleotides long, representing translating ribosomes in distinct states, differentially stabilized by specific elongation inhibitors. We find that the balance of small and large footprints varies by codon and is correlated with translation speed. The ability to visualize conformational changes in the ribosome during elongation, at single-codon resolution, provides a new way to study the detailed kinetics of translation and a new probe with which to identify the factors that affect each step in the elongation cycle. Ribosome profiling, or sequencing of ribosome-protected mRNA fragments, in yeast. We assay ribosome footprint sizes and positions in three conditions: untreated yeast (3 replicates) and yeast treated with translation inhibitors cycloheximide (2 replicates) and anisomycin (2 biological replicates, one technical replicate). We also treat yeast with 3-aminotriazole to measure the effect of limited histidine tRNAs on ribosome footprint size and distribution (two treatment durations).
2014-06-10 | E-GEOD-58321 | biostudies-arrayexpress
Project description:Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We focus on multiple myeloma cells exposed to bortezomib, a first-line chemotherapy and proteasome inhibitor. In the absence of drug effects, we found that direct measurement of protein synthesis by pSILAC correlated well with indirect measurement of synthesis from ribosome footprint density. This correlation, however, broke down under bortezomib-induced stress. By developing a statistical model integrating longitudinal proteomic and mRNA-seq measurements, we found that proteomics could directly detect global alterations in translational rate caused by bortezomib; these changes are not detectable by ribosomal profiling alone. Further, by incorporating pSILAC data into a gene expression model, we predict cell-stress specific proteome remodeling events. These results demonstrate that pSILAC provides an important complement to ribosome profiling in measuring proteome dynamics.
2017-05-18 | GSE69047 | GEO
Project description:Here, we use ribosome-footprint profiing and mRNA-seq to determine the average ribosome density on each gene in S. cerevisiae. We then perform quantitative modeling to identify the molecular determinants of ribosome density. Analysis of S. cerevisiae
2013-12-19 | E-GEOD-53313 | biostudies-arrayexpress
Project description:Ribosome footprint profiling is a high throughput sequencing based technique that provides detailed and global views of translation in living cells. An essential part of this technology is removal of unwanted, normally abundant, ribosomal RNA sequences in order to save on sequencing costs. The most effective commercial solution (Ribo-Zero) has been discontinued and a number of new, experimentally distinct commercial applications have emerged on the market. Here we evaluated several commercially available alternatives designed for RNA-seq of human samples and find them unsuitable for ribosome footprint profiling. We instead recommend the use of custom-designed biotinylated oligos, which were widely used in early ribosome profiling studies. Importantly, we warn that depletion solutions based on targeted nuclease cleavage significantly perturb the high-resolution information that can be derived from the data, and thus do not recommend their use for any applications that require precise determination of the ends of RNA fragments.
2020-03-27 | GSE147324 | GEO
Project description:Silencing of FMR1 and loss of its gene product FMRP results in Fragile X Syndrome. FMRP binds brain mRNAs and inhibits polypeptide elongation. Using ribosome profiling of the hippocampus, we find that ribosome footprint levels in Fmr1-deficient tissue mostly reflect changes in RNA abundance. Profiling over a time course of ribosome runoff in wildtype tissue reveals a wide range of ribosome translocation rates; on many mRNAs, the ribosomes are stalled. Sucrose gradient ultracentrifugation of hippocampal slices after ribosome runoff reveals that FMRP co-sediments with stalled ribosomes; and its loss results in decline of ribosome stalling on specific mRNAs. One such mRNA encodes SETD2, a lysine methyltransferase that catalyzes H3K36me3. ChIP-Seq demonstrates that loss of FMRP alters the deployment of this epigenetic mark on chromatin. H3K36me3 is associated with alternative pre-RNA processing, which we find occurs in an FMRP-dependent manner on transcripts linked to neural function and autism spectrum disorders.
2020-03-31 | GSE143329 | GEO
Project description:Members of the third domain of life, the Archaea, are ubiquitous in all environments on Earth but remain understudied in many aspects including regulatory processes of the central dogma. Archaea present unique biology because they utilize a mosaic of molecular features from both Bacteria and Eukarya, along with unique features. The advent of a high-throughput view of the translation landscape via ribosome profiling in the Bacteria and the Eukarya has illuminated the complexity and previously underappreciated regulation of translation (i.e. translation efficiency, ribosome surveillance, etc.) that potentially has large scale effects on cellular functionality. Here, we developed ribosome profiling in a model archaeon, Haloferax volcanii and elucidated the translational landscape for the first time in the third domain of life. We coupled ribosome profiling with translation inhibitors to: (a) determine the size of the archaeal ribosome footprint, (b) systematically assign translation states of the ribosome to footprint lengths in a mostly leaderless transcriptome, (c) experimentally induce ribosome pauses and clarify the pausing landscape comprehensively, (d) identify putative novel proteins, including small open reading frames (smORFs), and (e) provide evidence that many genes initiate on putative alternative translation start sites (paTSS) around and within open reading frames (ORFs), demonstrating how a microorganism with a gene dense genome can produce proteins with distinct functions using the same gene.
2020-04-27 | GSE138990 | GEO