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TranscriptomicsThe ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome pr...
ORGANISM(S): Homo sapiens 
2012-07-26 | E-GEOD-37744 | biostudies-arrayexpress
TranscriptomicsAdvancing Trypanosoma brucei genome annotation through ribosome profiling and spliced leader mapping
Since the initial publication of the trypanosomatid genomes, curation has been ongoing. Here we apply the technique of ribosome profiling to Trypanosoma brucei, identifying 223 new coding regions by virtue of ribosome occupancy in the corresponding transcripts. A small number of these putative genes...
ORGANISM(S): Trypanosoma brucei 
2015-12-22 | E-GEOD-72463 | biostudies-arrayexpress
ProteomicsSystematic detection of amino acid substitutions in proteomes reveals a mechanistic basis of ribosome errors and selection for translation fidelity
The translation machinery and the genes it decodes co-evolved to achieve production throughput and accuracy. Nonetheless translation errors are frequent and they affect physiology and protein evolution. Mapping translation errors in proteomes and understanding their causes was hindered by lack of a ...
ORGANISM(S): Escherichia coli 
2019-07-29 | PXD014341 | Pride
Translation  ribosome errors  mispairing  misloading  mass spectrometry 
TranscriptomicsCorrecting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]
The molecular mechanisms of ethanol toxicity and tolerance in bacteria, while important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and revealed multiple mechanisms of tolerance, but it remains d...
ORGANISM(S): Escherichia coli 
2014-06-18 | E-GEOD-56372 | biostudies-arrayexpress
TranscriptomicsDual randomization of oligonucleotides to reduce the bias in ribosome-profiling libraries
Protein translation is at the heart of cellular metabolism and its in-depth characterization is key for many lines of research. Recently, ribosome profiling became the state-of-the-art method to quantitatively characterize translation dynamics at a transcriptome-wide level. However, the strategy of ...
ORGANISM(S): Saccharomyces cerevisiae 
2016-08-01 | E-GEOD-84746 | biostudies-arrayexpress
TranscriptomicsWidespread Co-translational RNA Decay Reveals Ribosome Dynamics
It is generally assumed that mRNAs undergoing translation are protected from decay. Here, we show that mRNAs are, in fact, co-translationally degraded. This is a widespread and conserved process affecting most genes, where 5′–3′ transcript degradation follows the last translating ribosome, producing...
ORGANISM(S): Schizosaccharomyces pombe 
2015-06-04 | E-GEOD-63120 | biostudies-arrayexpress
TranscriptomicsCorrecting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Terminator_Readthrough_RNAseq]
The molecular mechanisms of ethanol toxicity and tolerance in bacteria, while important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and revealed multiple mechanisms of tolerance, but it remains d...
ORGANISM(S): Escherichia coli 
2014-06-18 | E-GEOD-56407 | biostudies-arrayexpress
GenomicsSystematic detection of amino acid substitutions in proteome reveals a mechanistic basis of ribosome errors and selection for translation fidelity
Systematic detection of amino acid substitutions in proteome reveals a mechanistic basis of ribosome errors and selection for translation fidelity
PRJNA528937 | ENA
ProteomicsTranslation Error Clusters Induced by Aminoglycoside Antibiotics
Aminoglycoside antibiotics (AGAs) target the ribosome and induce mistranslation, yet which translation errors induce bacterial cell death is unclear. The analysis of cellular proteins by quantitative mass spectrometry shows that bactericidal AGAs induce not only single translation errors, but also c...
ORGANISM(S): Escherichia Coli 
2021-04-06 | PXD019328 | panorama
GenomicsSystematic detection of amino acid substitutions in proteome reveals a mechanistic basis of ribosome errors and selection for translation fidelity
The protein translation machinery and the genes it decodes co-evolved to achieve production throughput and accuracy. Nonetheless translation errors are frequent and they affect physiology, fitness and protein evolution. Mapping translation errors in proteomes and understanding their causes was hinde...
ORGANISM(S): Escherichia coli Escherichia coli BW25113 
2019-04-18 | GSE128812 | GEO
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