Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A coding sequence-embedded principle governs translational reading frame fidelity

ABSTRACT: A coding sequence-embedded principle governs translational reading frame fidelity

PROVIDER: PRJNA318051 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3356523.fastq.gz	Fastqsanger.gz
	SRR3356524.fastq.gz	Fastqsanger.gz
	SRR3356525.fastq.gz	Fastqsanger.gz
	SRR3356526.fastq.gz	Fastqsanger.gz
	SRR3356527.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 7

Similar Datasets

A coding sequence-embedded principle governs translational reading frame fidelity

Project description:Upon initiation at an AUG start codon, the ribosome must maintain the correct reading frame for hundreds of codons in order to produce functional proteins. Although some sequence elements are able to trigger programmed ribosomal frameshifting (PRF), very little is known how the ribosome normally prevents spontaneous frameshift errors. Using high resolution ribosome profiling data sets, we discovered that the translating ribosome uses the 3’ end of 18S rRNA to scan the AUG-like codons after the decoding process. The internal mRNA:rRNA interaction not only contributes to predominant translational pausing, but also provides a post-decoding mechanism to safeguard the ribosome in the correct reading frame. Partially eliminating the AUG-like “sticky” codons in the reporter message leads to increased +1 frameshift errors. Remarkably, mutating the highly conserved CAU triplet of 18S rRNA globally changes codon “stickiness”. Further supporting the role of “sticky” sequences in reading frame maintenance, the codon composition of open reading frames is highly optimized across eukaryotic genomes by minimizing the appearance of AUG-like codons in the frame 2. These results suggest an important layer of information embedded within the protein coding sequences that instructs the ribosome to ensure reading frame fidelity during translation.

2016-04-12 | GSE80156 | GEO

A Coding Sequence-Embedded Principle Governs Translational Reading Frame Fidelity.

Project description:Upon initiation at a start codon, the ribosome must maintain the correct reading frame for hundreds of codons in order to produce functional proteins. While some sequence elements are able to trigger programmed ribosomal frameshifting (PRF), very little is known about how the ribosome normally prevents spontaneous frameshift errors that can have dire consequences if uncorrected. Using high resolution ribosome profiling data sets, we discovered that the translating ribosome uses the 3' end of 18S rRNA to scan the AUG-like codons after the decoding process. The postdecoding mRNA:rRNA interaction not only contributes to predominant translational pausing, but also provides a retrospective mechanism to safeguard the ribosome in the correct reading frame. Partially eliminating the AUG-like "sticky" codons in the reporter message leads to increased +1 frameshift errors. Remarkably, mutating the highly conserved CAU triplet of 18S rRNA globally changes the codon "stickiness". Further supporting the role of "sticky" sequences in reading frame maintenance, the codon composition of open reading frames is highly optimized across eukaryotic genomes. These results suggest an important layer of information embedded within the protein-coding sequences that instructs the ribosome to ensure reading frame fidelity during translation.

| S-EPMC6750092 | biostudies-literature

Alternative Reading Frame expression in POLG gene

Project description:POLGARF is an upstream Alternative Reading Frame in POLG gene partially overlapping POLG sequence. To obtain POLGARF peptide reference spectra POLGARF was overexpressed in HEK293T and HEK293F cells .

2021-09-08 | PXD016007 | Pride

MOTS-c: A Novel Peptide Encoded by a Short Mitochondrial Open Reading Frame Regulates Metabolic Homeostasis

Project description:Mitochondria are known to be functional organelles, but their role as a signaling unit is increasingly being appreciated. The recent identification of a short open reading frame (sORF) in the mitochondrial DNA (mtDNA) that encodes a signaling peptide, humanin, suggests the possible existence of additional sORFs in the mtDNA that yield bioactive peptides. Here we report the identification of a sORF within the mitochondrial 12S rRNA encoding a 16-amino-acid peptide named MOTS-c (mitochondrial open-reading-frame of the twelve S rRNA -c) that regulates insulin sensitivity and metabolic homeostasis. MOTS-c is detected in various tissues and in circulation in an age-dependent manner. Its primary target organ appears to be the skeletal muscle and its cellular actions inhibit the folate cycle and its tethered de novo purine biosynthesis, causing a significant accumulation of AICAR levels concomitantly with AMPK activation. MOTS-c treatment in mice prevented age-dependent and high-fat diet-induced insulin resistance, as well as diet-induced obesity. These results suggest that mitochondria may be more actively engaged in regulating metabolic homeostasis than previously recognized, through the production of peptides encoded within its genome that act at the cellular and organismal level. Human embryonic kidney cells (HEK293 cell line) were cultured in 10-cm dishes in 7 mL of phenol-free DMEM supplemented with 10% FBS and incubated with water (controls) or the 16-amino-acid peptide mitochondrial open-reading-frame of the twelve S rRNA-c (MOTS-c, 10 uM) for 4 or 72 hours prior to RNA extraction.

2015-03-07 | E-GEOD-65068 | biostudies-arrayexpress

Translation rescue by targeting Ppp1r15a upstream open reading frame in vivo

Project description:Translation rescue by targeting Ppp1r15a upstream open reading frame in vivo

| PRJNA790822 | ENA

Temperature-dependent regulation of upstream open reading frame translation in s. cerevisiae

Project description:Temperature-dependent regulation of upstream open reading frame translation in s. cerevisiae

| PRJNA564290 | ENA

MOTS-c: A Novel Peptide Encoded by a Short Mitochondrial Open Reading Frame Regulates Metabolic Homeostasis

2015-03-07 | GSE65068 | GEO

Translation rescue by targeting Ppp1r15a upstream open reading frame in vivo

Project description:The eIF2 initiation complex is central to maintaining a functional translation machinery. Extreme stress such as life-threatening sepsis exposes vulnerabilities in this tightly regulated system, resulting in an imbalance between the opposing actions of kinases and phosphatases on the main regulatory subunit eIF2α. Here, we report that translation shutdown is a hallmark of established sepsis-induced kidney injury brought about by excessive eIF2α phosphorylation and sustained by blunted expression of the counterregulatory phosphatase subunit Ppp1r15a. We determined that the blunted Ppp1r15a expression persists because of the presence of an upstream open reading frame (uORF). Overcoming this barrier with genetic approaches enabled the derepression of Ppp1r15a, salvaged translation and improved kidney function in an endotoxemia model. We also found that the loss of this uORF has broad effects on the composition and phosphorylation status of the immunopeptidome that extended beyond the eIF2α axis. Collectively, our findings define the breath and potency of the highly conserved Ppp1r15a uORF and provide a paradigm for the design of uORF-based translation rheostat strategies. The ability to accurately control the dynamics of translation during sepsis will open new paths for the development of therapies at codon level precision.

2021-12-22 | GSE191262 | GEO

Circadian ribosome profiling reveals a role for the Period2 upstream opening reading frame in sleep

Project description:Circadian ribosome profiling reveals a role for the Period2 upstream opening reading frame in sleep

| PRJNA832792 | ENA

Circadian ribosome profiling reveals a role for the Period2 upstream opening reading frame in sleep.

Project description:Circadian ribosome profiling reveals a role for the Period2 upstream opening reading frame in sleep.

| PRJNA967742 | ENA