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Translation complex profiling for bacteria [Ribo-seq]

ABSTRACT: Translation complex profiling for bacteria [Ribo-seq]

PROVIDER: PRJNA506724 | ENA |

REPOSITORIES: ENA

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Translation complex profiling for bacteria [Ribo-seq]

Project description:Ribosomes were arrested during initiation, elongation and termination complex formation using formaldehyde crosslinking. The complex protected footprints were isolated after MNase treatment and sequenced.

2019-09-16 | GSE122870 | GEO

Determine the effects of METTL16 on global translation efficiency via ribosome profiling (Ribo-seq)

Project description:METTL16 is a member of methyltransferase like (METTL) family. Unlike well-studied METTL3 and METTL14, we found a much higher percentage of METTL16 is localized in the cytosol. The subcellular distribution holds the ability to potentiate translation efficiency. Via Far-western blotting and Co-Immunoprecipitation (Co-IP) assays, we have identified the direct interactions between METTL16 and eukaryotic initiation factor 3 (eIF3) a and b. Via cross-linking immunoprecipitation and qPCR (CLIP-qPCR), we have discovered the direct associations between METTL16 and rRNAs. The METTL16-eIF3a/b and METTL16-rRNAs interactions induce the binding between eIF3 and 18S rRNA, promote the formation of 43S preinitiation complex, and eventually expedite translation initiation, the rate-limiting step of translation. To determine the exact effects of METTL16 on translation efficiency, we performed ribosome profiling (Ribo-seq) with HEK293T upon CRISPR-Cas9-induced METTL16 knockout. To guarantee the repeatability and avoid any potential off-target effects, we included 3 distint sgRNAs against METTL16.

2021-10-28 | GSE156796 | GEO

Genome-Wide Translation Profiling by Ribosome-Bound tRNA Capture

Project description:In the ribosome complex, tRNA is a critical element of mRNA translation. We reported a new technology for profiling ribosome-embedded tRNAs and their modifications. With the method, we generated a comprehensive survey of the quanity and quality of intra-ribosomal tRNAs (Ribo-tRNA-seq). Ribo-tRNA-seq can provide new insights on translation control mechanism in diverse biological contexts.

2018-03-19 | E-MTAB-6576 | biostudies-arrayexpress

eIF1-eIF4G1 inhibitors uncover alternative translation activation of stress-response genes via enhanced ribosome loading and 5’UTR translation [Ribo-Seq and Ti-Seq]

Project description:The Ribo-seq and TI-seq analysis following i14G1s (eI1-eIF4G1 inhibitors) treatments uncover opposing roles of eIF1-eIF4G1 and eIF4E-eIF4G1 in scanning-dependent and independent translation. Furthermore, i14G1s inhibition of eIF4G1-eIF1 resulted in translation activation of ER/UPR stress-response genes via enhanced ribosome loading, elevated 5’UTR translation at near cognate AUGs, and unexpected concomitant upregulation of coding-region translation.

2022-07-07 | GSE166742 | GEO

Ribo-seq of Arabidopsis mTRAN double mutants

Project description:mTRAN proteins are are plant specific-components of the mitoribosome. To asses of loss-of-function mtran1 mtran2 double mutants show decreased translation rates, we performed ribosome footprinting coupled to RNA-seq (Ribo-seq).

2023-09-01 | E-MTAB-13059 | biostudies-arrayexpress

Ribo-seq (Ribosome profiling) analyses in human multiple myeloma cells

Project description:Detection of protein translation status at the gene level. Ribo-seq experiment of human multiple myeloma cells including NAT10 overexpression and controls were conducted.

2021-11-30 | GSE155917 | GEO

Retapamulin-assisted Ribo-seq reveals the alternative bacterial proteome

Project description:Unorthodox rules of extracting genetic information enable proteome expansion without increasing the genome size. The use of alternative translation initiation sites achieves this goal by allowing production of more than one protein from a single gene. Although several such examples have been serendipitously found in bacteria, genome-wide experimental mapping of alternative translation start sites has been unattainable. We found that the antibiotic retapamulin specifically arrests initiating ribosomes at start codons of the genes. Retapamulin treatment followed by Ribo-seq analysis (Ribo-RET) not only allowed mapping of conventional initiation sites at the beginning of the annotated Escherichia coli genes but, strikingly, it also revealed putative alternative internal start sites in a number of genes. Experimental evidence demonstrated that the internal start codons can be recognized by the ribosomes and direct translation initiation in vitro and in vivo. Proteins, whose translation is initiated at an internal in-frame and out-of-frame start sites, can be functionally important and contribute to the ‘alternative’ bacterial proteome. In addition to proteome expansion, the internal start sites may play regulatory role in gene expression.

2019-03-04 | GSE122129 | GEO

Translation Complex Profiling analysed using sequencing (TCP-seq) applied to fission yeast cells (Schizosaccharomyces pombe)

Project description:Translation complexes are stabilised in vivo using formaldehyde. Cells are lysed, and cell extracts are treated with RNase I to produce protected RNA fragments (FPs or footprints). Extracts are then run through sucrose gradients to separate small ribosomal subunits and full ribosomes. FPs are isolated from each of these fractions and analysed by sequencing. Note this is a modified version of ribo-seq (a.k.a. ribosome profiling)

2022-12-02 | E-MTAB-12264 | biostudies-arrayexpress

Improved Ribo-seq enables identification of cryptic translation events.

Project description: Not available

| S-EPMC6152898 | biostudies-literature

Ribo-seq on K562 and HepG2 cells

Project description:Deep sequencing methods have matured to comprehensively detect the full set of transcribed loci, but there is a gap to determine the function of the resulting highly complex transcriptomes. To this end, we have developed a new approach named ORFquant to annotate and quantify translation at the single open reading frame (ORF) level using Ribo-seq data.

2020-04-26 | GSE129061 | GEO

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