Landscapes of gene translation in hepatocellular carcinoma tumors revealed by ribosome profiling
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE112705 | GEO | 2019/06/14
REPOSITORIES: GEO
Similar Datasets
Project description:Landscapes of gene translation in hepatocellular carcinoma tumors revealed by ribosome profiling
| PRJNA448763 | ENA
Project description:The development of the ribosome profiling (ribo-seq) technique has enabled the measurement of translation at a genome-wide level. There are several variants of the ribosome profiling technique that use different translation inhibitors. The regular ribo-seq utilizes Cycloheximide (CHX), a translation elongation inhibitor to freeze all translating ribosomes. In contrast to CHX, the translation inhibitor lactimidomycin (LTM) and harringtonine (Harr) have a much stronger effect on initiating ribosomes. The use of these inhibitors allows for the global mapping of translating initiating sites (TISs) when they are coupled with ribosome profiling (TI-seq). We have developed a computational tool to detect and/or quantitatively compare translation initiation from TI-seq data, and predict novel ORFs from regular CHX-based ribo-seq data. Two replicates of CHX-based ribo-seq experiments and one Harr based ribo-seq were performed in HEK293 cells for confirming the ORFs predicted using public available data.
2018-01-22 | GSE94460 | GEO
Project description:Many mammalian proteins have circadian cycles of production and degradation, but de novo transcription is only responsible for a small fraction of this rhythmicity. We used ribosome profiling to quantify RNA translation in liver from circadian-entrained mice transferred to constant darkness conditions over a 24-h period and compared translation levels to absolute protein production for 16 circadian proteins. We observed a delay between translation and peak protein levels for several circadian genes covering a wide range of translation efficiencies. We found extensive binding of ribosomes to upstream open reading frames (uORFs) in circadian mRNAs, including the core clock gene Period2 (Per2). Increased uORFs in 5' UTRs was associated with decreased ribosome binding in downstream ORFs and reduced expression of synthetic reporter constructs in vitro and in single cells. Mutation of the Per2 uORF increased luciferase and fluorescence reporter expression in 3T3 cells without altering phase or period. Genomic Per2 uORF mutation using CRISPR/Cas9 increased PER2 expression in PER2:Luc MEFs and reduced sleep in Per2 uORF mutant mice. These results suggest that post-transcriptional processes shape translation of mRNA transcripts, which can impact physiological rhythms and sleep.
2023-05-05 | GSE201732 | GEO
Project description:This study aims to investigate the dysregulation of RNA translation and identify functional non-canonical open reading frames (ORFs) as potential targets for medulloblastoma treatment. The study involves ribosome profiling and RNAseq of medulloblastoma tissues and cell lines to observe the translation of non-canonical ORFs. Multiple CRISPR-Cas9 screens will be used to identify functional non-canonical ORFs implicated in medulloblastoma cell survival.
| EGAD00001011193 | EGA
Project description:This study aims to investigate the dysregulation of RNA translation and identify functional non-canonical open reading frames (ORFs) as potential targets for medulloblastoma treatment. The study involves ribosome profiling and RNAseq of medulloblastoma tissues and cell lines to observe the translation of non-canonical ORFs. Multiple CRISPR-Cas9 screens will be used to identify functional non-canonical ORFs implicated in medulloblastoma cell survival.
| EGAD00001011192 | EGA
Project description:The delineation of genes in bacteria has remained an important challenge because prokaryotic genomes are often tightly packed frequently resulting in overlapping genes. We hereby present a de novo approach called REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION) to delineate translated open reading frames (ORFs) in bacteria independent of (available) genome annotation. By deep sequencing of ribosome protected mRNA fragments (RPF) to map translating ribosomes across the entire genome, REPARATION takes advantage of the recently developed ribosome profiling (Ribo-seq) technique. REPARATION starts by traversing the entire genome to generate all possible ORFs and then collects their corresponding RPF signal information. Based on a growth curve model to estimate minimum ORF read density and Ribo-seq RPF coverage, thresholds indicative of translation is estimated. Finally, our algorithm applies a random forest model to build a classifier to classify putative protein coding ORFs. We evaluated the performance of REPARATION on 3 annotated bacterial species using in-house generated Ribo-seq data and matching N-terminal and shotgun proteomics data next to publically available Ribo-seq data. In all cases, about 80% of the ORFs predicted by REPARATION were previously annotated as protein coding. While 13-20% were variants of previously annotated ORFs and about 3-4% point to novel translated ORFs within intergenic or other regions previously annotated as non-coding. Without stringent length restrictions REPARATION was able to identify several small ORFs (sORFs). Multiple supportive evidence from matching MS data and sequence conservation analysis was obtained to validate predicted ORFs.
2017-01-30 | GSE91066 | GEO
Project description:The Caulobacter cell cycle includes sequential differentiation of the cell poles and an asymmetric cell division yielding distinct daughter cells. RNA-seq and ribosome profiling were used to measure global messenger RNA (mRNA) abundance and translation levels throughout the Caulobacter cell cycle revealing translational control in 51% of cell cycle-regulated genes. Ribosome profiling levels were temporally regulated for ten proteins encoding asymmetrically localized multi-protein assemblies that specify cell fate upon cell division, with five ORFs being regulated with a >2 fold contribution from the translation efficiency. Individual ORFs within 198 operons undergo different cell cycle patterns of translation efficiency, allowing decoupling of the expression of these co-transcribed units. This work reveals that, in addition to transcriptional control, there is prevalent translational control of cell cycle-regulated genes, providing a framework for a multi-level program of cell cycle control that generates daughter cells of different fates.
2016-04-20 | GSE68200 | GEO
Project description:Protein concentrations evolve under greater evolutionary constraint than mRNA levels. In addition, translation efficiency of mRNA populations represents the chief determinant of basal protein concentrations. This raises a fundamental question as to how mRNA and protein levels are actively coordinated in dynamic systems responding to acute physiological stimuli. This report examines the contributions of mRNA abundance and translation efficiency to protein output in cells responding to oxygen stimulus. We show that alternative translation efficiencies, not mRNA levels, represent the major adaptive mechanism that governs the cellular response to perturbations in [O2]. This phenomenon is coordinated by eIF4F under atmospheric [O2] and the previously uncharacterized hypoxic eIF4F (eIF4FH) under low [O2]. The oxygen-regulated remodeling of translation efficiency enables oxygenated and hypoxic cells to produce surprisingly divergent translatomes of similar complexity, with minimal dependence on mRNA levels. Changes in mRNA concentrations observed between normoxic and hypoxic cells are likely neutral, as they are during evolution. We propose that mRNAs contain hard-wired translation efficiency determinants for their triage by the translation apparatus on [O2] stimulus.
2016-02-05 | PXD003037 | Pride
Project description:Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here, we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but employs duplex-specific nuclease as a convenient, bias-free, species-independent way to reduce rRNA contamination. Our protocol typically produces high levels of triplet periodicity, facilitating the detection of coding sequences, including upstream, downstream and overlapping open reading frames (ORFs). This feature also allows the identification of an alternative ribosome conformation evident during termination of protein synthesis. To test the effectiveness of DSN in ribosome profiling, we generated Ribo-Seq libraries from mouse tissue culture cells and from the green alga Chlamydomonas reinhardtii.
2015-10-16 | E-MTAB-2934 | biostudies-arrayexpress
Project description:Although protein synthesis dynamics has been studied both with theoretical models and by profiling ribosome footprints, the determinants of ribosome flux along open reading frames (ORFs) are not fully understood. Combining measurements of protein synthesis rate with ribosome footprinting data, we here inferred translation initiation and elongation rates for over a thousand ORFs in exponentially-growing wildtype yeast cells. We found that the amino acid composition of synthesized proteins is as important a determinant of translation elongation rate as parameters related to codon and tRNA adaptation. We did not find evidence of ribosome collisions curbing the protein output of yeast transcripts, either in high translation conditions associated with exponential growth, or in strains in which deletion of individual ribosomal protein genes leads to globally increased or decreased translation. Slow translation elongation is characteristic of RP-encoding transcripts, which have markedly lower protein output compared to other transcripts with equally high ribosome densities.
2019-09-10 | PXD014357 | Pride