Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryo reveals hundreds of conserved translating sORFs
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ABSTRACT:
PROVIDER: PRJEB13069 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1328563_1.fastq.gz | Fastqsanger.gz | |||
| ERR1328563_2.fastq.gz | Fastqsanger.gz | |||
| ERR1328564_1.fastq.gz | Fastqsanger.gz | |||
| ERR1328564_2.fastq.gz | Fastqsanger.gz | |||
| ERR1328565_1.fastq.gz | Fastqsanger.gz |
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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:Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryo reveals hundreds of conserved translating sORFs
| PRJDB4646 | ENA
Project description:<p><strong>BACKGOUND:</strong> Ultra-processed food (UPF) accounts for a majority of calories consumed in the United States, but the impact on human health remains unclear. We aimed to identify poly-metabolite scores in blood and urine that are predictive of UPF intake.</p><p><strong>METHODS AND FINDINGS:</strong> Of the 1082 Interactive Diet and Activity Tracking in AARP (IDATA) Study (clinicaltrials.gov ID NCT03268577) participants, aged 50-74 years, who provided biospecimen consent, n=718 with serially collected blood and urine and one to six 24-hour dietary recalls (ASA-24s), collected over 12-months, met eligibility criteria and were included in the metabolomics analysis. Ultra-high performance liquid chromatography with tandem mass spectrometry was used to measure >1000 serum and urine metabolites. Average daily UPF intake was estimated as percentage energy according to the Nova system. Partial Spearman correlations and Least Absolute Shrinkage and Selection Operator (LASSO) regression were used to estimate UPF-metabolite correlations and build poly-metabolite scores of UPF intake, respectively. Scores were tested in a previously conducted randomized, controlled, crossover-feeding trial (clinicaltrials.gov ID NCT03407053) of 20 subjects who were admitted to the NIH Clinical Center and randomized to consume ad libitum diets that were 80% or 0% energy from UPF for 2 weeks immediately followed by the alternate diet for 2 weeks; eligible subjects were between 18-50 years old with a body mass index of >18.5 kg/m2 and weight-stable. IDATA participants were 51% female, and 97% completed 4 ASA-24s. Mean intake was 50% energy from UPF. UPF intake was correlated with 191 (of 952) serum and 293 (of 1044) 24-hour urine metabolites (FDR-corrected P-value < 0.01), including lipid (n=56 serum, n=22 24-hour urine), amino acid (n=33, 61), carbohydrate (n=4, 8), xenobiotic (n=33, 70), cofactor and vitamin (n= 9, 12), peptide (n=7, 6), and nucleotide (n=7, 10) metabolites. Using LASSO regression, 28 serum and 33 24-hour urine metabolites were selected as predictors of UPF intake; biospecimen-specific scores were calculated as a linear combination of selected metabolites. Overlapping metabolites included (S)C(S)S-S-methyl cysteine sulfoxide (rs= -0.19, -0.23), N2-N5-diacetylornithine (rs= -0.26, -0.27), pentoic acid (rs= -0.28, -0.31), and N6-carboxymethyllysine (rs=0.15, 0.21). Within the cross-over feeding trial, the poly-metabolite scores differed, within individual, between UPF diet phases (P-value for paired t-test <0.001). IDATA Study participants were older US adults whose diets may not be reflective of other populations.</p><p><strong>CONCLUSIONS:</strong> Poly-metabolite scores, developed in IDATA participants with varying diets, are predictive of UPF intake and could advance epidemiological research on UPF and health. Poly-metabolite scores should be evaluated and iteratively improved in populations with a wide range of UPF intake.</p>
2025-07-12 | MTBLS12705 | MetaboLights
Project description:Human cells have evolved multiple quality control mechanisms to ensure protein homeostasis by detecting aberrant mRNAs and protein products which are condemned for rapid decay. Translating ribosomes that run into poly(A) tails are terminally stalled, followed by ribosome recycling and rapid decay of the truncated nascent polypeptide via the ribosome-associated quality control (RQC). Here, we demonstrate that the conserved RNA-binding E3 ubiquitin ligase Makorin Ring Finger Protein 1 (MKRN1) acts as a novel sensor of poly(A) sequences to initiate ribosome stalling in RQC. Using individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP), we show that MKRN1 is positioned upstream of A-rich stretches and poly(A) tails in mRNAs via interaction with the cytoplasmic poly(A)-binding protein (PABP). Ubiquitin remnant profiling uncovers PABP and ribosomal protein RPS10 as well as multiple translational regulators as main targets of MRKN1-mediated ubiquitylation. The modified lysine in RPS10 is distinct from the main target sites of ZNF598, the second E3 ubiquitin ligase involved in initial ribosome stalling, indicating that multiple modifications need to converge to prevent promiscuous ubiquitylation of lysine-translating ribosomes. We propose that MKRN1 serves as a first line of poly(A) recognition at the RNA level to prevent erroneous protein products and maintain proteome integrity.
2019-08-19 | PXD011772 | Pride
Project description:There is growing recognition that small open reading frames (sORFs) encoding peptides shorter than 100 amino acids are an important class of functional elements in the eukaryotic genome, with several already identified to play critical roles in growth, development, and disease. However, our understanding of their biological importance has been hindered owing to the significant technical challenges limiting their annotation. Here we combined ultra-deep sequencing of ribosome-associated poly-adenylated RNAs with rigorous conservation analysis to identify a comprehensive population of translated sORFs during early Drosophila embryogenesis. In total, we identify 399 sORFs, including those previously annotated but without evidence of translational capacity, those found within transcripts previously classified as non-coding, and those not previously known to be transcribed. Further, we find, for the first time, evidence for translation of many sORFs with different isoforms, suggesting their regulation is as complex as longer ORFs. Furthermore, many sORFs are found not associated with ribosomes in late-stage Drosophila S2 cells, suggesting that many of the translated sORFs may have stage-specific functions during embryogenesis. These results thus provide the first comprehensive annotation of the sORFs present during early Drosophila embryogenesis, a necessary basis for a detailed delineation of their function in embryogenesis and other biological processes.
| S-EPMC5144680 | biostudies-literature
Project description:To discover new regulators of Regulatory Particle Assembly Chaperone (RPAC) translation, we identified RNA-binding proteins (RBPs) with increased recruitment to translating WT FGH17 mRNAs compared to non-translatable FGH17-40ntΔ mRNAs in vivo. To this end, we first treated yeast cells with rapamycin to stimulate translation of FGH17 mRNAs. Ribosomes were locked on mRNAs using cycloheximide and UV-crosslinking covalently linked the RNA and any bound proteins together. We next used anti-FLAG beads to immunoprecipitate translated FGH17 protein, as well as any translating FGH17-mRNA complexes where locked ribosomes had already synthesized one or both N-terminal FLAG tags. As FGH17-40ntΔ mRNAs are not translated, these samples should only immunoprecipitate proteins that bind non-specifically to the anti-FLAG beads. Based on the prediction that potential regulators of RPAC translation would be UV crosslinked to FGH17 mRNA within the 5’ UTR and upstream of locked translating ribosomes, we used RNases to specifically elute these potential regulators. We then identified the proteins in the RNase elution by tandem mass tag (TMT)-based quantitative proteomics.
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Project description:Ultra high resolution breakpoint mapping using custom oligonucleotide arrays and array painting Keywords: Breakpoint mapping
2006-11-01 | GSE4297 | GEO
Project description:Ultra high resolution breakpoint mapping using custom oligonucleotide arrays and array painting The two derivative chromosomes from 4 patients with balanced translocations were flow sorted, differentially labelled and hybridised to custom oligonucleotide arrays designed to cover the potential breakpoint region at high resolution. Single hybridisations with no replicates.
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Project description:Poly(A)-ClickSeq is a new methodology for the sequencing of the 3'UTR/poly(A) tail junction of RNA. We analysed both wild-type and CF25Im knock-down HeLa cells in culture using Poly(A)-ClickSeq to find the distribution of poly(A) sites in these samples and determine the role of CF25Im in poly(A) site selection (alternative poly-adenylation, APA).
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