Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA258156 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To verify unannotated translated open reading frames (utORFs) identified from Drosophila melanogaster, we collected data to target them.
2022-04-06 | PXD032197 | Pride
Project description:Pervasive functional translation of noncanonical open reading frames
| PRJNA544411 | ENA
Project description:Identification of translating small open reading frames (sORFs) through deep sequecing of ribosome-associated poly-adenylated RNA and conservation analysis in early Drosophila embryo
2017-03-05 | E-MTAB-4571 | biostudies-arrayexpress
Project description:Small open reading frames (smORFs) can have important regulatory roles and give rise to stable proteins, yet their discovery based on sequence-based predictions and proteomics has been challenging. Ribosome profiling (Ribo-seq) data can provide valuable experimental evidence of RNA translation. Stringent analysis of P-sites, representing 1.3 billion high-confidence ribosome locations, revealed 5308 uORFs, 1652 smORFs in lincRNAs and 807 dORFs that are translated in humans. We here provide a comprehensive database of Ribo-seq smORFs for a more complete understanding of the translated human genome.
2022-07-18 | GSE182372 | GEO
Project description:Small open reading frames (smORFs) can have important regulatory roles and give rise to stable proteins, yet their discovery based on sequence-based predictions and proteomics has been challenging. Ribosome profiling (Ribo-seq) data can provide valuable experimental evidence of RNA translation. Stringent analysis of P-sites, representing 1.3 billion high-confidence ribosome locations, revealed 5308 uORFs, 1652 smORFs in lincRNAs and 807 dORFs that are translated in humans. We here provide a comprehensive database of Ribo-seq smORFs for a more complete understanding of the translated human genome.
2022-07-18 | GSE182371 | GEO
Project description:SEPs (Small open reading frames-encoded peptides) identified from 11 time-points, which were chosen during drosophila’s complete life cycle.
2021-04-08 | PXD025249 | iProX
Project description:Ribosome profiling and high-throughput sequencing provide unprecedented opportunities for the analysis of mRNA translation. Using this novel method, several studies have demonstrated the widespread role of short upstream reading frames in translational control as well as slower elongation at the beginning of open reading frames in response to stress. Based on the initial studies, the importance of adding or omitting translation inhibitors, such as cycloheximide, was noted as it markedly affected ribosome coverage profiles. For that reason, many recent studies omitted translation inhibitors in the culture medium. Here, we investigate the influence of ranging cycloheximide concentrations on ribosome profiles in Saccharomyces cerevisiae and demonstrate that increasing the drug concentration can overcome some of the artifacts. We subjected cells to various manipulations and show that neither oxidative stress nor heat shock nor amino acid starvation affect translation elongation. Instead, the observations in the initial studies are the result of cycloheximide-inflicted artifacts. Likewise, we find little support for short upstream reading frames to be involved in wide-spread protein synthesis regulation under stress conditions. Our study highlights the need for better standardization of ribosome profiling methods. Ranging concentrations of cycloheximide and various stress contitions were tested with Ribo-seq
2014-08-01 | E-GEOD-59573 | biostudies-arrayexpress
Project description:Ribosome profiling revealed translation outside of canonical coding sequences (CDSs) including translation of short upstream open-reading frames (ORFs), long non-coding RNAs, ORFs in UTRs or ORFs in alternative reading frames. Ribo-seq but also bioinformatics-based prediction and RNA-sequencing reported translation of thousands of ORFs derived from non-translated regions (NTRs). Although such ORFs gained increased attention over the years, their actual coding potential remains debated as protein products of only a fraction of them were identified by mass spectrometry. Here, we introduced a new workflow to discover translation products of NTRs at a large-scale. We combined reducing sample complexity (by enriching N-terminal peptides of cytosolic proteins as such peptides are ideal proxies for translation) with and extend search space (combining the sequences of UniProt proteins, UniProt isoforms and publicly available Ribo-seq data) reasoning that this combination increased chances of identifying proteins from NTRs. Further, we introduced rigorous data analysis and results curation workflows to cope with the increased complexity of the search space and to mine identified peptides. This stringent filtering approach was found essential to retain confident translational evidence at the peptide level for NTRs. We show that theoretically our strategy facilitates the detection of translation events of transcripts from NTRs, but experimentally less than 1% of all identified peptides might originate from such translation events.
2022-07-12 | PXD030601 | Pride
Project description:The Translation of Non-Canonical Open Reading Frames Controls Mucosal Immunity
| PRJNA494404 | ENA
Project description:Meiosis is a complex developmental process that generates haploid cells from diploid progenitors. We measured mRNA abundance and protein production through yeast sporulation and found strong temporal control for most genes, achieved through both mRNA levels and translational regulation. Monitoring the timing of protein production revealed novel factors involved in recombination and helped to illuminate the molecular basis of the broad restructuring of meiotic cells. We also found a strong increase in noncanonical translation at short open reading frames (sORFs) on unannnotated transcripts and upstream regions of known transcripts (uORFs). Ribosome occupancy at near-cognate uORFs was associated with more efficient ORF translation; while some AUG uORFs, often on regulated leader extensions, acted comptetitively. This work reveals a pervasive role for meiotic translational control and great complexity in genomic coding. Fine mapping of gene expression through meiosis reveals extensive regulation of protein synthesis and widespread non-canonical translation.
2012-01-06 | E-GEOD-34082 | biostudies-arrayexpress