Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribosome sequencing of adenocarcinoma cells - control and FKBP10 SH

ABSTRACT: We report ribosome sequencing of A549 pulmonary adenocarcinomic human alveolar basal epithelial cells. This was carried out with unmodified cells as well as cells with FKBP10 knocked down with shRNA. This data was paired with RNASeq on the same cells and the transcriptional profiles were assessed to understand the effect of FKBP10 SH. This was done firstly by assessing alterations in gene-wide summary plots of global changes in transcription. These demonstrate pervasive extra pausing at the start site and a loss in translational elongation product, largely associated with ribosomal protein genes. Pairing this data with corresponding RNASeq allowed us to look at translational efficiency (TE), which showed the lower rate of elongation in the knockdown was principally attributable to a loss in translational efficiency since transcription levels were largely unchanged.

ORGANISM(S): Homo sapiens

PROVIDER: GSE129654 | GEO | 2020/04/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Comparative Ribo-Seq of Staphylococcus aureus harboring A2058-unmodified ribosomes and m6A2058-modified ribosomes

Project description:A total of 10 cDNA libraries were constructed, representing 3 and 2 independent biological replicates of S. aureus strain KES34 (unmodified ribosomes) and KES30 (m6A2058-modified ribosomes), respectively. Translational efficiency (RPF/mRNA ratios), total mRNA abundance and ribosome density of each ORFs were calculated.

2024-01-16 | GSE168265 | GEO

Causal signals between codon bias, mRNA structure and the efficiency of translation and elongation

Project description:Ribosome profiling data reports on the distribution of translating ribosomes, at steady-state, with codon-level resolution. We present a robust method to extract codon translation rates and protein synthesis rates from these data, and identify causal features associated with elongation and translation efficiency in physiological conditions in yeast. We show that neither elongation rate nor translational efficiency is improved by experimental manipulation of the abundance or body sequence of the rare AGG tRNA. Deletion of three of the four copies of the heavily used ACA tRNA shows a modest efficiency decrease that could be explained by other rate-reducing signals at gene start. This suggests that correlation between codon bias and efficiency arises as selection for codons to utilize translation machinery efficiently in highly translated genes. We also show a correlation between efficiency and RNA structure calculated both computationally and from recent structure probing data, as well as the Kozak initiation motif, which may comprise a mechanism to regulate initiation. We test whether tRNA abundance affects elongation or translation efficiency by changing the tRNA levels through deletion or over expression and measuring the ribosomal dwell time at each codon using a robust statistical method that accounts for flow conservation.

2015-01-05 | E-GEOD-63789 | biostudies-arrayexpress

RNA-seq using human SH-SY5Y neuroblastoma cells used for SILAC experiment

Project description:To measure translational efficiency in FMRP depletion, we purified RNAs from either wild-type or FMR1-knockout (FMR1-KO) SH-SY5Y cells generated for SILAC coupled to LC-MS/MS analysis and performed RNA-seq to quantitate mRNA abundance to normalize their protein abundance.

2022-10-30 | GSE197221 | GEO

Decrypting the functional design of unmodified translation elongation factor P

Project description:Stalling of ribosomes due to consecutive proline motifs during polypeptide synthesis is a challenge faced by organisms across all kingdoms. To overcome this, bacteria employ translation elongation factor P (EF-P), while archaea and eukaryotes rely on a/eIF5A. Typically, these elongation factors become active only after undergoing post-translational modifications (PTMs) such as ß-lysinylation, (deoxy-)hypusinylation, rhamnosylation, or 5-aminopentanolyation. An exception to this rule is found in EF-P members of the PGKGP-subfamily, which remain unmodified. However, the mechanism behind the ability of certain bacteria to bypass metabolically and energetically costly PTMs, thus retaining active EF-P, remains unclear. In this study, we investigated the design principles governing the full functionality of unmodified EF-Ps in Escherichia coli. We first screened for naturally unmodified EF-Ps that are active in an E. coli reporter strain. We identified EF-P from Rhodomicrobium vannielii capable of rescuing the growth deficiencies and changes in the proteome of E. coli ΔepmA mutant lacking the gene for the modifying EF-P-(R)-ß-lysine ligase. We then identified specific amino acids in domain I of the unmodified EF-P variant that affected its activity. Ultimately, we transferred these functional properties to other marginally active members of the PGKGP EF-P subfamily, resulting in fully functional unmodified variants in E. coli. These results have not only implications for the improved heterologous expression of polyproline-containing proteins in E. coli but offer applications for other bacterial hosts. Understanding the mechanisms that underlie the functionality of unmodified EF-P provides insights into cellular adaptations to optimize protein synthesis.

2024-04-08 | PXD044929 | Pride

Causal signals between codon bias, mRNA structure and the efficiency of translation and elongation

2015-01-05 | GSE63789 | GEO

Elongation Control

Project description:Translational control by elongation in yeast

| PRJEB22674 | ENA

Clarifying the translational pausing landscape in bacteria by ribosome profiling

Project description:The rate of protein synthesis varies according to the mRNA sequence in ways that affect gene expression. Global analysis of translational pausing is now possible with ribosome profiling. Here, we revisit an earlier report that Shine-Dalgarno sequences are the major determinant of translational pausing in bacteria. Using refinements in the profiling method as well as biochemical assays, we find that SD motifs have little (if any) effect on elongation rates. We argue that earlier evidence of pausing arose from two factors. First, in previous analyses, pauses at Gly codons were difficult to distinguish from pauses at SD motifs. Second, and more importantly, the initial study preferentially isolated long ribosome-protected mRNA fragments that are enriched in SD motifs. These findings clarify the landscape of translational pausing in bacteria as observed by ribosome profiling. Ribosome profiling (three replicates) and RNAseq (two replicates) of E. coli MG1655

2016-01-13 | E-GEOD-72899 | biostudies-arrayexpress

Transcription Rate Strongly Affects Splicing Fidelity and Co-transcriptionality in Budding Yeast

Project description:The functional consequences for alternative splicing of altering the transcription rate have been the subject of intensive study in mammalian cells but less is known about effects on splicing of changing the transcription rate in yeast. We present several lines of evidence showing that slow RNA polymerase II elongation increases both co-transcriptional splicing and splicing efficiency and faster elongation reduces co transcriptional splicing and splicing efficiency in budding yeast, suggesting that splicing is more efficient when co-transcriptional. Moreover, we demonstrate that altering RNA polymerase II elongation rate in either direction compromises splicing fidelity, and we reveal that splicing fidelity depends largely on intron length together with secondary structure and splice site score. These effects are notably stronger for the highly expressed ribosomal protein coding transcripts. We propose that transcription by RNA polymerase II is tuned to optimise the efficiency and accuracy of ribosomal protein gene expression, while allowing flexibility in splice site choice with the nonribosomal protein transcripts.

2017-11-25 | GSE99161 | GEO

HOT3/eIF5B1 confers Kozak motif-dependent translational control of photosynthesis-associated nuclear genes for chloroplast biogenesis

Project description:Photosynthesis requires chloroplasts, where most proteins are nucleus-encoded and produced via cytoplasmic translation. The translation initiation factor eIF5B gates the transition from initiation (I) to elongation (E), and the Kozak motif is associated with translation efficiency, but their relationship is previously unknown. Here, with ribosome profiling, we determined the genome-wide I-E transition efficiencies. We discovered that the most prevalent Kozak motif is associated with high I-E transition efficiency in Arabidopsis, rice, and wheat, thus implicating the Kozak motif in facilitating the I-E transition. Indeed, the effects of most Kozak motifs, including the most effective ones, depend on HOT3/eIF5B1 in Arabidopsis. HOT3 preferentially promotes the translation of photosynthesis-associated nuclear genes in a Kozak motif-dependent manner, which explains the chloroplast defects of hot3 mutants. Our study reveals an evolutionarily-conserved link between the Kozak motif and eIF5B-mediated translational I-E efficiency and elucidates a HOT3-mediated translational control of nuclear photosynthesis genes for chloroplast biogenesis.

2024-10-03 | GSE212855 | GEO