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Ribosome Profiling of mouse skin squamous tumours

ABSTRACT: Purpose: Ribosome profiling has revolutionized systems-based analysis and which produces a “global snapshot” of all the ribosomes translationally active in a cell at a particular moment. The goals of this study are to first apply ribosome profiling to in vivo samples for the first time and in particular to stem cells and tumours and second to determine which mRNAs are being actively translated in these particular situations. Although much is known about gene expression regulation, little is known about how protein translation regulation can affect stem cell differentiation and tumour progression. Methods: several replicates of ribosome and mRNA profiles of wild-type (WT) and NSun2 -/- mouse skin squamous tumours were generated by deep sequencing, using Illumina HiSeq platform. Results: Our analyses reveal that activation of stress response pathways in vivo drives both a global reduction of protein synthesis and altered translation of specific mRNAs that together promote stem cell functions and tumourigenesis.

ORGANISM(S): Mus musculus

PROVIDER: GSE72066 | GEO | 2016/06/16

SECONDARY ACCESSION(S): PRJNA292862

REPOSITORIES: GEO

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Ribosome Profiling of mouse skin squamous tumours

Project description:Purpose: Ribosome profiling has revolutionized systems-based analysis and which produces a âglobal snapshotâ of all the ribosomes translationally active in a cell at a particular moment. The goals of this study are to first apply ribosome profiling to in vivo samples for the first time and in particular to stem cells and tumours and second to determine which mRNAs are being actively translated in these particular situations. Although much is known about gene expression regulation, little is known about how protein translation regulation can affect stem cell differentiation and tumour progression. Methods: several replicates of ribosome and mRNA profiles of wild-type (WT) and NSun2 -/- mouse skin squamous tumours were generated by deep sequencing, using Illumina HiSeq platform. Results: Our analyses reveal that activation of stress response pathways in vivo drives both a global reduction of protein synthesis and altered translation of specific mRNAs that together promote stem cell functions and tumourigenesis. Ribosome profiles of wild-type (WT) and NSun2 -/- mouse skin squamous tumours

2016-06-16 | E-GEOD-72066 | biostudies-arrayexpress

A systematic survey of PRMT interactomes reveals key roles of arginine methylation in the global control of RNA splicing and translation [Ribo-Seq]

Project description:We used Ribo-seq to determine how PRMT inhibition affects translation of different mRNAs, This analysis can generate a “snapshot” of all mRNAs that are occupied by active ribosomes (i.e., undergoing active translation) in a cell at a particular condition.

2022-06-30 | GSE153142 | GEO

Project description:mRNAs with NSUN2-dependent translation efficiency and the molecular features of NSUN2 target mRNAs

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Analysis of the translational landscape of Arabidopsis mitochondria

Project description:Messenger RNA translation is a complex process that is still poorly understood in eukaryotic organelles like mitochondria. Growing evidence indicate though that mitochondrial translation differs from its bacterial counterpart in many key aspects. In this analysis, we used the ribosome profiling technology to generate a genome-wide snapshot view of mitochondrial translation in Arabidopsis. We show that, unlike in humans, most Arabidopsis mitochondrial ribosomes footprints measure 27 and 28 bases. We also reveal that respiratory subunits encoding mRNAs show much higher ribosome association than other mitochondrial mRNAs, implying that they are translated to higher levels. Homogenous ribosome densities were generally detected within each respiratory complex except for complex V where higher ribosome coverage corroborate with higher needs in specific subunits. In complex I respiratory mutants, a slight reorganization of mitochondrial mRNAs ribosome association was detected involving an increase in ribosome densities on certain ribosomal protein encoding transcripts and a reduction in the translation of a few complex V mRNAs. Altogether, our observations reveal that plant mitochondrial translation is a dynamic process and that translational control is important for gene expression in plant mitochondria. This study paves the way for future advances in the understanding of translation in higher plant mitochondria.

2018-05-31 | GSE104028 | GEO

Location and Function of Cytosine-5 Methylation in RNA

Project description:Mutations in the cytosine-5 RNA methyltransferase NSun2 can cause neurodevelopmental disorders and symptoms commonly found in patients with Dubowitz-like syndrome. Some tRNAs are known to be methylated NSun2, however the occurrence of cytosine-5 methylation (m5C) in other RNA biotypes is still under debate. Location in RNA and function of m5C has not been studied yet. This study is aimed at identifying new m5C methylated RNA biotypes, as well as the location at specific structures or sequences and the ultimate biological function. The impact of the loss of NSun2-mediated methylation is also determined by comparing gene expression data with the global cytosine-5 RNA methylome in Dubowitz-like syndrome patients. We also use ribosomal profiling to assess the impact of the loss and rescue of Nsun2-mediated cytosine-5 RNA methylation on translation rates and ribosome occupancy.

| phs000645 | dbGaP

Time resolved ribosome profiling study of oxygen and glucose deprivation of rat pheochromocytoma cells

Project description:Oxygen and glucose metabolism plays a pivotal role in many (patho)physiological conditions. In particular, oxygen and glucose deprivation (OGD) occurs during ischemia and stroke, resulting in extensive tissue injury and cell death. We applied time-resolved ribosome profiling technique to assess early events at the level of gene expression in rat pheochromocytoma PC12 cells during short-term OGD. Most substantial alterations in transcripts levels and their translation were seen to occur in the first 20 minutes of OGD. The rapid adaptation of translation apparatus to OGD is global and involves altered elongation and initiation rates. We also observed salient and reproducible alterations in ribosome densities of individual mRNAs such as increased translation of particular upstream Open Reading Frames (uORFs); induced site-specific arrests of the ribosomes and synthesis of extended protein isoforms. Ribosome profiling (with mRNA-seq sequencing) was carried out at 0,20,40 and 60 minutes of OGD. Two biological replicates were used.

2015-04-10 | E-GEOD-60752 | biostudies-arrayexpress

Stem cell function and sensitivity to genotoxic stress is controlled by protein translation rates

Project description:Whether protein synthesis and cellular stress response pathways interact to control stem cell functions is currently unknown. Here, we show that skin stem cells synthesise less protein than their immediate progenitors in vivo, even when forced to proliferate in a tumour model. Our analyses reveal that activation of stress response pathways drives both a global reduction of protein synthesis and altered translation of specific mRNAs that together promote stem cell functions and tumourigenesis. Mechanistically we show that inhibition of post-transcriptional cytosine-5 methylation locks stem cells in this distinct translational inhibition programme. Paradoxically, this stress-induced translation inhibition renders stem cells hypersensitive to genotoxic stress, as tumour regeneration after treatment with 5-fluorouracil is blocked. Thus, stem cells must revoke translation inhibition pathways to regenerate a tissue or tumour. This SuperSeries is composed of the SubSeries listed below.

2016-06-16 | E-GEOD-72067 | biostudies-arrayexpress

Transfer RNA (tRNA) processing and RNA m5C-methylation profiles of mouse skin squamous tumours

Project description:Purpose: High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, such those derived from tRNAs. Also recent advances in high-throughput RNA sequencing has revealed the complex RNA modification landscape and the complex role these nucleosides modifactions have in cell signalling, stem cell biology, development and cancer. The goal of this study is to establish how m5C-tRNA methylation and tRNA-derived small RNAs can affect stem cell fucntion in cancer. Methods: four replicates of tRNAs and RNA buisulphite sequencing of wild-type (WT) and NSun2 -/- mouse skin squamous tumours were generated by deep sequencing, using Illumina HiSeq platform. Results: Our analyses reveal that inhibition of post-transcriptional cytosine-5 methylation locks stem cells in this distinct translational inhibition programme that results in tumour progression but that also sentizes cancer cells to genotoxic stress. Transfer RNA (tRNA) sequencing and RNA Bisulphite sequencing of wild-type (WT) and NSun2 -/- mouse skin squamous tumours

2016-06-16 | E-GEOD-72065 | biostudies-arrayexpress

Multiple links between 5-methylcytosine content of mRNA and translation

Project description:5-methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA. In pursuit of potential links of m5C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise. We obtained ~1,000 candidate m5C sites in the wider transcriptome, most of which were found in exonic regions of mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCap and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m5C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in mRNA and noncoding RNA. Candidate m5C sites in mRNAs are enriched in 5’UTRs and near start codons, and commonly embedded in a local context reminiscent of the NSUN2-dependent m5C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that non-conversion levels, at bulk and for many individual sites, were inversely correlated with ribosome association. Altogether, these findings emphasise the major role of NSUN2 in making this mark transcriptome-wide and further substantiate a functional interdependence of cytosine methylation level with mRNA translation

2020-03-09 | GSE140995 | GEO

A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis [Polysome-seq]

Project description:Ribosomal defects perturb stem cell differentiation, causing diseases called ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, we discovered three RNA helicases are required for ribosome biogenesis and for Drosophila oogenesis. Loss of these helicases, which we named Aramis, Athos and Porthos, lead to aberrant stabilization of p53, cell cycle arrest and stalled GSC differentiation. Unexpectedly, Aramis is required for efficient translation of a cohort of mRNAs containing a 5’-Terminal-Oligo-Pyrimidine (TOP)-motif, including mRNAs that encode ribosomal proteins and a conserved p53 inhibitor, Novel Nucleolar protein 1 (Non1). The TOP-motif co-regulates the translation of growth-related mRNAs in mammals. As in mammals, the La-related protein co-regulates the translation of TOP-motif containing RNAs during Drosophila oogenesis. Thus, a previously unappreciated TOP-motif in Drosophila responds to reduced ribosome biogenesis to co-regulate the translation of ribosomal proteins and a p53 repressor, thus coupling ribosome biogenesis to GSC differentiation.

2022-03-24 | GSE171349 | GEO

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