Determinants of ribosome density in yeast
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE53313 | GEO | 2013/12/19
SECONDARY ACCESSION(S): PRJNA231673
REPOSITORIES: GEO
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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 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: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:Post-transcriptional control is crucial for regulating protein expression, both basally and in response to extracellular cues. Proper signal transduction requires tight control of both response induction and termination. One way protein expression might be attenuated is by targeting mRNAs to translation-dependent degradation (TDD), thus making any increase in protein expression self-limiting. However, the extent to which TDD is a general mechanism for limiting protein expression is currently unknown. Here we describe a comprehensive analysis of basal and signal-induced TDD in mouse primary CD4 T cells. Our data indicate that most cellular transcripts are decayed to some extent in a translation-dependent manner, both in resting and activated cells. Analysis of transcript features revealed that 3’UTR length and ribosome density are major determinants of the magnitude of TDD as well as GC content and amino acid identity. Consistently, upon T cell activation, all transcripts that undergo changes in ribosome density display a corresponding change in their level of TDD. Surprisingly, the amplitude of translation-independent mRNA decay appears as a mirror image of TDD. Moreover, translation-independent decay also responds to changes in ribosome density upon T cell activation but in the opposite direction to those observed for TDD. Our data demonstrate a strong interconnection between mRNA translation and decay in mammalian cells. Furthermore they indicate that ribosome loading is a major determinant of the pathway by which transcripts are degraded within cells
2024-03-01 | GSE159300 | GEO
Project description:Post-transcriptional control is crucial for regulating protein expression, both basally and in response to extracellular cues. Proper signal transduction requires tight control of both response induction and termination. One way protein expression might be attenuated is by targeting mRNAs to translation-dependent degradation (TDD), thus making any increase in protein expression self-limiting. However, the extent to which TDD is a general mechanism for limiting protein expression is currently unknown. Here we describe a comprehensive analysis of basal and signal-induced TDD in mouse primary CD4 T cells. Our data indicate that most cellular transcripts are decayed to some extent in a translation-dependent manner, both in resting and activated cells. Analysis of transcript features revealed that 3’UTR length and ribosome density are major determinants of the magnitude of TDD as well as GC content and amino acid identity. Consistently, upon T cell activation, all transcripts that undergo changes in ribosome density display a corresponding change in their level of TDD. Surprisingly, the amplitude of translation-independent mRNA decay appears as a mirror image of TDD. Moreover, translation-independent decay also responds to changes in ribosome density upon T cell activation but in the opposite direction to those observed for TDD. Our data demonstrate a strong interconnection between mRNA translation and decay in mammalian cells. Furthermore they indicate that ribosome loading is a major determinant of the pathway by which transcripts are degraded within cells
2024-03-01 | GSE159299 | GEO
Project description:Post-transcriptional control is crucial for regulating protein expression, both basally and in response to extracellular cues. Proper signal transduction requires tight control of both response induction and termination. One way protein expression might be attenuated is by targeting mRNAs to translation-dependent degradation (TDD), thus making any increase in protein expression self-limiting. However, the extent to which TDD is a general mechanism for limiting protein expression is currently unknown. Here we describe a comprehensive analysis of basal and signal-induced TDD in mouse primary CD4 T cells. Our data indicate that most cellular transcripts are decayed to some extent in a translation-dependent manner, both in resting and activated cells. Analysis of transcript features revealed that 3’UTR length and ribosome density are major determinants of the magnitude of TDD as well as GC content and amino acid identity. Consistently, upon T cell activation, all transcripts that undergo changes in ribosome density display a corresponding change in their level of TDD. Surprisingly, the amplitude of translation-independent mRNA decay appears as a mirror image of TDD. Moreover, translation-independent decay also responds to changes in ribosome density upon T cell activation but in the opposite direction to those observed for TDD. Our data demonstrate a strong interconnection between mRNA translation and decay in mammalian cells. Furthermore they indicate that ribosome loading is a major determinant of the pathway by which transcripts are degraded within cells
2024-03-01 | GSE159295 | GEO
Project description:Determinants of ribosome density in yeast
| PRJNA231673 | ENA
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:mRNAs are generally assumed to be loaded instantly with ribosomes upon entry into the cytoplasm. To measure ribosome density on nascent mRNA, we developed nascent Ribo-Seq (nRibo-Seq) by combining Ribo-Seq with progressive 4-thiouridine labelling. In mouse macrophages, we experimentally determined, for the first time, the lag between the appearance of nascent RNA and its association with ribosomes, which was calculated to be 20 - 22 min for bulk mRNA, and approximated the time it takes for mRNAs to be fully loaded with ribosomes to be 41 - 44 min. Notably, ribosomal loading time is adapted to gene function as rapid loading was observed with highly regulated genes. The lag and ribosomal loading time correlate positively with ORF size and mRNA half-life, and negatively with tRNA adaptation index. Similar results were obtained in mouse embryonic stem cells, where the lag in ribosome loading was even more pronounced with 35 - 38 min. We validated our measurements after stimulation of macrophages with lipopolysaccharide, where the lag between cytoplasmic and translated mRNA leads to uncoupling between input and ribosome-protected fragments. Uncoupling is stronger for mRNAs with long ORFs or half-lives, a finding we also confirmed at the level of protein production by nascent chain proteomics. As a consequence of the lag in ribosome loading, ribosome density measurements are distorted when performed under conditions where mRNA levels are far from steady state expression, and transcriptional changes affect ribosome density in a passive way. This study uncovers an unexpected and considerable lag in ribosome loading, and provides guidelines for the interpretation of Ribo-Seq data taking passive effects on ribosome density into account.
2021-06-22 | PXD026828 | Pride
Project description:Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we here inferred translation initiation and elongation rates for over a thousand ORFs in exponentially-growing wildtype yeast cells. We found that the amino acid composition of synthesized proteins is as important a determinant of translation elongation rate as parameters related to codon and tRNA adaptation. We did not find evidence of ribosome collisions curbing the protein output of yeast transcripts, either in high translation conditions associated with exponential growth, or in strains in which deletion of individual ribosomal protein genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output compared to other transcripts with equally high ribosome densities.
2019-09-10 | PXD014357 | Pride