Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

ABSTRACT: To understand the contribution of mRNA synthesis and degradation rates towards setting protein concentrations, we performed RNA-sequencing based measurements of mRNA abundance and degradation to facilitate comparisons with recently collected proteomic datasets (Mori 2021) in the same E. coli strain.

ORGANISM(S): Escherichia coli K-12

PROVIDER: GSE205717 | GEO | 2022/06/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Sequencing of metabolically labeled transcripts in single cells from RPE1-FUCCI cells and murine intestinal organoids.

Project description:Measurements of metabolically labeled transcripts in single cells for estimation of mRNA synthesis and degradation rates throughout the cell cycle and intestinal organoid differentiation.

2020-03-05 | GSE128365 | GEO

Analysing the effect of cellular energy levels on codon-specific ribosome occupancy in vivo

Project description:The aim of this study is to evaluate how cellular energy levels shape codon-specific decoding and affect codon-mediated mRNA degradation. To this end we made use of HT5P-seq (Zhang & Pelechano, 2021, PMID:35474692) in S. cerevisiae to footprint the ribosome of co-translationally degraded mRNAs in vivo upon swift changes in the concentration of intracellular ATP and other energy metabolites.

2024-03-08 | GSE216524 | GEO

First-Principles Model to Evaluate Quantitatively the Long-Life Behavior of Cellulose Acetate Polymers.

Project description: Not available

| S-EPMC8014918 | biostudies-literature

A first-principles phase field method for quantitatively predicting multi-composition phase separation without thermodynamic empirical parameter.

Project description: Not available

| S-EPMC6671953 | biostudies-literature

Mori soil bacteria

Project description:Mori soil bacteria Raw sequence reads

| PRJNA562039 | ENA

Synthesis and degradation of FtsZ quantitatively predict the first cell division in starved bacteria.

Project description: Not available

| S-EPMC6217170 | biostudies-literature

Bacteria

Project description:Elucidation of degradation pathway of Green algal polysaccharide ulvan

| PRJDB7540 | ENA

Bacteria

Project description:Study for bacterial humic substance-degradation genes and pathways

| PRJNA514400 | ENA

Modelling global mRNA dynamics during Drosophila embryogenesis reveals a relationship between mRNA degradation and P-bodies

Project description:Regulation of mRNA degradation is critical for a diverse array of cellular processes and developmental cell fate decisions. Although many methods for determining mRNA half-lives rely on transcriptional inhibition or metabolic labelling, these manipulations can influence half-lives or introduce errors in the measurements. Here we use a non-invasive method for estimating mRNA half-lives globally in the early Drosophila embryo using a total RNA-seq time series and Gaussian process regression to model the dynamics of premature and mature mRNAs.

2022-11-15 | E-MTAB-11580 | biostudies-arrayexpress

Mechanisms of stop codon readthrough mitigation reveal principles of GCN1 mediated translational quality control

Project description:Readthrough into the 3′ untranslated region (3′UTR) of the mRNA results in the production of aberrant proteins. Metazoans efficiently clear readthrough proteins, but the underlying mechanisms remain unknown. Here, we show in C. elegans and mammalian cells that readthrough proteins are targeted by a coupled, two-level quality control pathway involving the BAG6 chaperone complex and the ribosome collision-sensing protein GCN1. Readthrough proteins with hydrophobic C-terminal extensions are recognized by SGTA-BAG6 and ubiquitylated by RNF126 for proteasomal degradation. Additionally, cotranslational mRNA decay initiated by GCN1 and CCR4/NOT limits the accumulation of readthrough products. Unexpectedly, selective ribosome profiling uncovered a general role of GCN1 in regulating translation dynamics when ribosomes encounter nonoptimal codons, a feature of 3′UTR sequences. Dysfunction of GCN1 results in mRNA and proteome imbalance, increasingly perturbing transmembrane proteins and collagens during aging. These results define GCN1 as a key factor acting during translation in maintaining protein homeostasis.

2023-06-09 | PXD037037 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data