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Drosophila melanogaster

ABSTRACT: Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryo reveals hundreds of conserved translating sORFs

PROVIDER: PRJDB4646 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR057103_1.fastq.gz	Fastqsanger.gz
	DRR057103_2.fastq.gz	Fastqsanger.gz
	DRR057104_1.fastq.gz	Fastqsanger.gz
	DRR057104_2.fastq.gz	Fastqsanger.gz
	DRR057105_1.fastq.gz	Fastqsanger.gz

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Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryo reveals hundreds of conserved translating sORFs

Project description:Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryo reveals hundreds of conserved translating sORFs

| PRJEB13069 | ENA

Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryo reveals hundreds of conserved translating sORFs

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

The RNA-binding ubiquitin ligase MKRN1 acts as a sensor for ribosome-associated quality control of poly(A)-translation

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

The small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti

Project description:Ribosome profiling was applied for the first time on S. meliloti to generate a translatome map. Our work reveals active translation for several ORFs including small ORFs (sORFs). In addition, our ribosome profiling data led to the discovery of several translated non-annotated sORFs. Translation of these non-annotated sORFs was validated by proteomics and western blotting.

2023-02-14 | GSE206492 | GEO

Ribosome profiling of Streptomyces griseus NBRC13350 and Streptomyces venezuelae ATCC15439

Project description:We performed ribosome profiling which is the deep-sequencing of mRNA fragments protected by translating ribosome for two Streptomyces species through different growth phases to provide the translatome data

2020-03-03 | GSE138278 | GEO

The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A)-translation

Project description:Human cells have evolved quality control mechanisms to ensure protein homeostasis by detecting and degrading aberrant mRNAs and protein products. A common source of aberrant mRNAs is premature polyadenylation, which can result in non-functional protein products. Translating ribosomes that encounter poly(A) sequences 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) promotes ribosome stalling at continuous A-tracts during 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 through an interaction with the cytoplasmic poly(A)-binding protein (PABP). Ubiquitin remnant profiling uncovered PABP and ribosomal protein RPS10 as well as additional translational regulators as main substrates of MRKN1. We propose that MKRN1 serves as a first line of poly(A) recognition at the mRNA level to prevent production of erroneous proteins, thus maintaining proteome integrity.

2019-08-19 | GSE122869 | GEO

Hypoxia-induced translational profiles of murine fetal liver derived macrophages (FLDM)

Project description:We report changes in total and translated poly(A) RNA in mouse fetal liver derived macrophages after exposure to hypoxia. We employed translating ribosome affinity purification (TRAP) to isolate polysomal RNA from mouse fetal liver derived macrophages after exposure to hypoxia.

2023-09-07 | GSE196966 | GEO

Hypoxia-induced translational profiles of murine bone marrow derived macrophages (BMDM)

Project description:We report changes in total and translated poly(A) RNA in mouse bone marrow derived macrophages after exposure to hypoxia. We employed translating ribosome affinity purification (TRAP) to isolate polysomal RNA from mouse bone marrow derived macrophages after exposure to hypoxia

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Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster

Project description:Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila melanogaster, but the importance of regulated readthrough in eukaryotes remains largely unexplored. Here, we present a ribosome profiling assay (deep sequencing of ribosome-protected mRNA fragments) for Drosophila melanogaster, and provide the first genome-wide experimental analysis of readthrough. Readthrough is far more pervasive than expected: the vast majority of readthrough events evolved within D. melanogaster and were not predicted phylogenetically. The resulting C-terminal protein extensions show evidence of selection, contain functional subcellular localization signals, and their readthrough is regulated, arguing for their importance. We further demonstrate that readthrough occurs in yeast and humans. Readthrough thus provides general mechanisms both to regulate gene expression and function, and to add plasticity to the proteome during evolution. 12 samples of Drosophila ribosome profiling and poly(A)+ mRNA-seq, including technical replicates in S2 cells, and biological replicates of 0-2 hour embryos

2013-12-05 | E-GEOD-49197 | biostudies-arrayexpress

Identification of polyA sites in Drosophila melanogaster

Project description:The 3' ends of most Drosophila melanogaster genes are poorly annotated or are determined by only a single EST or cDNA clone. To enhance the annotation of poly(A) site use in Drosophila, we performed deep sequencing on RNA isolated from 29 dissected tissues using an approach designed to enrich for poly(A) spanning reads. From these experiments, we identified 1.4 million poly(A) spanning reads leading to the identification of many new poly(A) sites and the identification of many tissue-specific poly(A) sites. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

2011-11-23 | GSE33905 | GEO

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