Head and Embryo 80S monosomes are much more translationally active than 80S in other tissues
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ABSTRACT:
PROVIDER: PRJNA1111495 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29021682.fastq.gz | Fastqsanger.gz | |||
| SRR29021683.fastq.gz | Fastqsanger.gz | |||
| SRR29021684.fastq.gz | Fastqsanger.gz | |||
| SRR29021685.fastq.gz | Fastqsanger.gz | |||
| SRR29021686.fastq.gz | Fastqsanger.gz |
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Project description:Translational regulation at the stage of initiation impacts the number of ribosomes translating each mRNA molecule. For example, multiple ribosomes can engage on a single mRNA forming a polysome, resulting in highly efficient protein synthesis. However, the translational activity of single 80S ribosomes on mRNA (monosomes) is less well understood, even though these 80S monosomes represent the dominant ribosomal complexes in many tissues. Here, we used cryo-EM to determine the translational activity of 80S monosomes across different tissues in Drosophila melanogaster. We discovered that while head and embryo 80S monosomes are highly translationally active, testis and ovary 80S monosomes are translationally inactive. RNA-Seq analysis of head monosome- and polysome-translated mRNAs, revealed that head 80S monosomes preferentially translate mRNAs with TOP motifs, short 5’-UTRs, short ORFs and are enriched for uORFs. Overall, these findings highlight that regulation of translation initiation, and therefore the number of ribosomes bound per mRNA, varies substantially across tissues.
2025-03-24 | GSE267425 | GEO
Project description:Fully assembled ribosomes exist in two populations: polysomes and monosomes. While the former has been studied extensively, to what extent translation occurs on monosomes and its importance for overall translational output remains controversial. Here, we used ribosome profiling to examine the translational status of 80S monosomes in Saccharomyces cerevisiae. We found that the vast majority of 80S monosomes are elongating, not initiating. Further, most mRNAs exhibit some degree of monosome occupancy, with monosomes predominating on nonsense-mediated decay (NMD) targets, upstream open reading frames (uORFs), canonical ORFs shorter than ~590 nucleotides and ORFs for which the total time required to complete elongation is substantially shorter than that required for initiation. Importantly, mRNAs encoding low-abundance regulatory proteins tend to be enriched in the monosome fraction. Our data highlight the importance of monosomes for the translation of highly regulated mRNAs. We examined the translational status of single 80S ribosomes using ribosome profiling, and compared these monosome footprints to both polysome ribosome footprints and general ribosome profiling. RNASeq libraries were also prepared from the overall sample input.
2016-02-11 | E-GEOD-76117 | biostudies-arrayexpress
Project description:Fully assembled ribosomes exist in two populations: polysomes and monosomes. While the former has been studied extensively, to what extent translation occurs on monosomes and its importance for overall translational output remains controversial. Here, we used ribosome profiling to examine the translational status of 80S monosomes in Saccharomyces cerevisiae. We found that the vast majority of 80S monosomes are elongating, not initiating. Further, most mRNAs exhibit some degree of monosome occupancy, with monosomes predominating on nonsense-mediated decay (NMD) targets, upstream open reading frames (uORFs), canonical ORFs shorter than ~590 nucleotides and ORFs for which the total time required to complete elongation is substantially shorter than that required for initiation. Importantly, mRNAs encoding low-abundance regulatory proteins tend to be enriched in the monosome fraction. Our data highlight the importance of monosomes for the translation of highly regulated mRNAs.
2016-02-11 | GSE76117 | GEO
Project description:The regulation of translation is crucial for cells to rapidly adapt to changing conditions. Although the transcriptional changes under inflammatory conditions are intensely studied, not much is known about translational changes. Therefore, this study aimed at identifying translationally deregulated targets in inflammatory settings.
2012-08-01 | GSE35022 | GEO
Project description:The regulation of translation is crucial for cells to rapidly adapt to changing conditions. Although the transcriptional changes under inflammatory conditions are intensely studied, not much is known about translational changes. Therefore, this study aimed at identifying translationally deregulated targets in inflammatory settings. MCF-7 cells were treated for 4h with the supernatants of U937 monocytes or TPA-activated U937 monocyte-derived macrophages and subjected to polysomal fractionation using sucrose gradients. Total RNA was collected simultaneously.
2012-07-31 | E-GEOD-35022 | biostudies-arrayexpress
Project description:Redefining the translational status of 80S monosomes
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Project description:The 80S ribosome was purified from tobacco (Nicotiana tabacum) leaves. part of the extract was analysed by mass spectrometry and the rest was used for cryo-EM investigations of the structure of the 80S ribosome.
2023-07-20 | PXD032330 | Pride
Project description:Upon the environmental changes, cells flexibly and rapidly alter the gene expression by the translation control. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is upregulated through the upstream open reading frame (uORF), which comprises only AUG and stop codons, in response to the shortage of boric acid. However, the molecular details of how the minimum uORF controls the translation of downstream main ORF depending on the boric acid concentration remained unclear. Here we showed that the 80S ribosome (80S) assembled at AUG-stop migrates into the subsequent RNA segment for downstream translation initiation and that the presence of boric acid impedes the process by stable confinement of eukaryotic release factor 1 (eRF1) on 80S on AUG-stop. Ribosome profiling along the in vitro-translated reporter mRNA revealed that the number of the ribosomes on AUG-stop and that along the downstream are anti-correlated in response to boric acid, reflecting the 80S scanning leaving AUG-stop for translation initiation from downstream ORF. Moreover, cryo-electron microscopy (cryo-EM) analysis revealed that, in the presence of boric acid, the initiator methionyl-tRNA (Met-tRNAi) in the P site stably contacts eRF1 in the A site on AUG-stop. In contrast, the absence of boric acid led to weaker eRF1 density, suggesting that eRF1 cannot be stably positioned without boric acid. Consistent with the structural features, the hydrolysis of Met-tRNAi on AUG-stop was accelerated by boric acid, which is likely to be the checkpoint for the subsequent 80S scanning of the downstream. Our results provide a molecular insight into the translation regulation by a minimum and environment-responsive uORF.
2023-09-20 | GSE189222 | GEO
Project description:Recent studies have revealed that the mRNA translation is punctuated by ribosomal pauses through the body of transcripts. However, little is known about its physiological significance and regulatory aspects. Here we present a multi-dimensional ribosome profiling approach to quantify the dynamics of initiation and elongation of 80S ribosomes across the entire transcriptome in mammalian cells. We show that a subset of transcripts have a significant pausing of 80S ribosome around the start codon, creating a major barrier to the commitment of translation elongation. Intriguingly, genes encoding ribosome proteins themselves exhibit an exceptionally high initiation pausing on their transcripts. Our studies also reveal that the initiation pausing is dependent on the 5M-bM-^@M-^Y untranslated region (5M-bM-^@M-^Y UTR) of mRNAs and subject to the regulation of mammalian target of rapamycin complex 1 (mTORC1). Thus, the initiation pausing of 80S ribosome represents a novel regulatory step in translational control mediated by nutrient signaling pathway. Monitor the translational status of transcriptome in mammalian cells under different conditions
2011-11-12 | E-GEOD-25626 | biostudies-arrayexpress
Project description:In response to environmental changes, cells flexibly and rapidly alter gene expression, through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is upregulated through upstream open reading frames (uORFs) that comprise only AUG and stop codons, in response to a shortage of boric acid in the environment. However, the molecular details of how the minimum uORF controls the translation of the downstream main ORF, in a boric acid concentration-dependent manner, have remained unclear. Here, combining ribosome profiling, TCP-Seq, structural analysis with cryo-electron microscopy, and biochemical assays, we showed that the 80S ribosome (80S) assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 (eRF1) on the 80S on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.
2023-09-19 | GSE223755 | GEO