Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1192995 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31565748.fastq.gz | Fastqsanger.gz | |||
| SRR31565749.fastq.gz | Fastqsanger.gz | |||
| SRR31565750.fastq.gz | Fastqsanger.gz | |||
| SRR31565751.fastq.gz | Fastqsanger.gz | |||
| SRR31565752.fastq.gz | Fastqsanger.gz |
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Project description:Currently, few studies have been performed on the function of peptides coding by open reading frames (ORFs) from annotated non-coding regions, especially the 3'-untranslated regions (3'-UTRs). The translated ORFs from 5'-UTRs (5'-ORFs) have been proved that they negatively affect the translation of their main ORFs, but there is little comprehension on 3'-ORFs. This study analyzed the genomic translational regulation events of ten development stages of maize anthers and demonstrated that the peptides translated by 5'- or 3'-ORFs may be misidentified isoforms and the 3'-ORFs may relate to anther sterility, such as the cloned APV1 locus, whose mutation caused male sterility. Furthermore, the global translation events indicated photosynthesis related genes enriched during Phase III, the binucleate microspore phase. The stomata in the anthers and low electron transport rate suggested that they can assimilate CO2 with low photosynthetic efficiency. This study proposed new avenues for the potential creation of male-sterile mutants using 3'-ORFs for hybrid breeding and new evidence of anther photosynthesis.
2026-04-27 | PXD068789 | Pride
Project description:Ribonuclease L (RNase L) is activated as part of the innate immune response and plays an important role in the clearance of viral infections. When activated, it endonucleolytically cleaves both viral and host RNAs, leading to a global reduction in protein synthesis. However, it remains unknown how widespread RNA decay, and consequent changes in the translatome, promote the elimination of viruses. To study how this altered transcriptome is translated, we assayed the global distribution of ribosomes in RNase L activated human cells with ribosome profiling. We found that RNase L activation leads to a substantial increase in the fraction of translating ribosomes in ORFs internal to coding sequences (iORFs) and ORFs within 5’ and 3’ UTRs (uORFs and dORFs). Translation of these alternative ORFs was dependent on RNase L’s cleavage activity, suggesting that mRNA decay fragments are translated to produce short peptides that may be important for antiviral activity.
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Project description:Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptideM-bM-^@M-^Pencoding genes in vertebrates, providing an entry point to define their function in vivo. Ribosome profiling experiments at five timepoints across zebrafish development in WT embryos
2014-04-04 | E-GEOD-53693 | biostudies-arrayexpress
Project description:Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptide‐encoding genes in vertebrates, providing an entry point to define their function in vivo.
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Project description:Ribosome profiling has revealed translation outside of canonical coding sequences (CDSs) including translation of short upstream ORFs, long non-coding RNAs, overlapping ORFs, ORFs in UTRs or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling and CRISPR-based screens showed that hundreds of ORFs derived from non-coding transcripts produce (micro)proteins and might be functional, while other studies failed to find evidence for such types of non-canonical translation events. In this study we tried to detect (and characterize) proteins originating from these non-translated regions (NTRs). We attempted to discover translation products from non-coding regions at large scale by reducing the overall sample complexity (by enriching cytosolic N-terminal peptides) and combined it with an extend search space (combining UniProt proteins, UniProt isoforms and publicly available Ribo-seq data). Reasoning that this strategy would increase the likelihood of identifying proteins from NTRs. Further, we introduced rigorous data analysis and results curation workflows. 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 we find that less than 1% of all identified peptides might originate from such translation events. However, one NTR protein was further characterized by Virotrap based interaction analysis. This resulted in several potential interaction partners associated with membranes and vesicle transport. Showing that the non-translated regions that do result in proteins might be functional.
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Project description:We provide sequences of maize chlroplast RNAs associated with non-PPR editing factors through immunoprecipitation. The accumulated sequences indicate expansive role in RNA processing and potential associations of OZ1-ORRM1 complexes with the ribosome and less efficiently translated mRNAs.
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Project description:The vast majority of bacterial open reading frames (ORFs) are identified by automated prediction algorithms. However, these algorithms fail to identify ORFs that deviate from the canonical features of ORFs such as a length of >50 codons, and the presence of an upstream Shine-Dalgarno sequence. Here, we use ribosome profiling approaches to experimentally identify actively translated ORFs in Mycobacterium tuberculosis. Most of the ORFs we identify have not been previously described, indicating that the M. tuberculosis transcriptome is pervasively translated. Moreover, the newly described ORFs are predominantly short, with many encoding proteins of ≤50 amino acids. The codon usage of the newly discovered ORFs suggests that most are not undergoing purifying selection, and hence are unlikely to contribute to cell fitness. Nevertheless, we identify ~90 new ORFs, with a median length of 52 codons, that bear the hallmarks of purifying selection. Thus, our data suggest that pervasive translation of short ORFs serves as a rich source for the evolution of new functional proteins
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Project description:Agilent oligonucleotide arrays were used to profile gene expression in dissected maize anthers of 3 types of male-sterile plants and their fertile siblings at four stages of development: after anther initiation, at the rapid mitotic proliferation stage, pre-meiosis, and meiotic prophase I. The male-sterile mutants (ms23, msca, and mac1) lack a range of normal cell types resulting from a temporal progression of anther failure. By combining the data sets from the comparisons between individual sterile and fertile anthers, candidate genes predicted to play important roles during maize anther development were assigned to stages and to likely cell types. Keywords: anther development, maize, male sterility 3 biological replicates of 3 different male-sterile mutants and their fertile siblings at 4 stages of anther development (36 arrays). Comparisons were done between male-sterile and fertile sibs at the same development stage.
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