Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

PROVIDER: PRJNA1115475 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR29203311.fastq.gz	Fastqsanger.gz
	SRR29203312.fastq.gz	Fastqsanger.gz
	SRR29203313.fastq.gz	Fastqsanger.gz
	SRR29203314.fastq.gz	Fastqsanger.gz
	SRR29203315.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 14

Similar Datasets

Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

Project description:Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

| PRJNA1132984 | ENA

Effect of specific G-quadruplex stabilization on gene expression and chromatin accessibility at gene promoters in Hela cells.

Project description:To investigate specific G-quadruplex stabilization in the regulation of gene expression and chromatin accessibility, we established HeLa cell lines in which each target g-quadruplexes has been stabilized.

2024-05-25 | GSE255625 | GEO

G4 quadruplex landscape and its regulation revealed by a new antibody capture method

Project description:Currently, the identification of G4 quadruplexes in vivo depends on a published and widely used G4-ChIP protocol (PMID: 29470465) that uses the anti-G4 antibody to captures the quadruplexes like regular chromatin. This method is challenged by some false positives and false negatives in G4-quadruplex capture. We have developed an antibody capture G4-ChIP (AbC G4-ChIP) method to overcome these challenges. The AbC G4-ChIP achieves (i) minimized in vitro artifacts during the incubation steps, and (ii) capture of G4-quadruplexes which are not protein-bound. We have applied the AbC G4-ChIP to study the regulatory effect of a CGG-repeat binding protein CGGBP1 on G4-quadruplex formation. The AbC G4-ChIP identifies inter-strand G/C-skew as a sequence property associated with CGGBP1-regulated G4-quadruplexes.

2024-03-20 | GSE202456 | GEO

Project description:L. Sativa mycorrhizal symbiosis allows to overcome phosphorus deficiency

| PRJNA1043852 | ENA

Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds

Project description:Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds

| PRJNA744571 | ENA

RNA polyadenylation and cellular ATP levels regulate the stability of RNAs in Escherichia coli

Project description:To investigate the extent of the effect of poly(A) polymerase (PAP I)-mediated polyadenylation on RNA stability, we performed the first genome-wide study of RNA stability in the absence of PAP I activity. Inactivation of the pcnB gene coding for PAP I led to a global stabilization of E. coli RNAs, with 1403 stabilized transcripts and only 4 destabilized. Stabilized RNAs were involved in essential cellular functions such as DNA replication and repair, translation, RNA degradation, central carbon metabolism but also in stress responses. Because PAP I is an ATP-consuming enzyme we wondered whether the RNA stabilization observed after inactivation of PAP I could also be related to changes in intracellular ATP levels. We demonstrated for the first time in E. coli, that lowering intracellular ATP levels below 1 µM/OD stabilizes RNAs. Although the ATP level was reduced by 20 % in the pcnB mutant on glucose, the ATP level was still too high to have any role in the observed RNA stabilization. However, in experiments where the ATP level was artificially strongly decreased, inactivation of PAP I by substrate availability was implicated in the stabilization mechanism of certain RNAs. This study clearly demonstrates that PAP I is at the crossroads of the regulation of RNA stability by energy status in E. coli cells.

2024-11-27 | GSE248472 | GEO

Translation elongation inhibitors stabilize select transcripts

Project description:The ribosome is central to cellular stress responses because it serves as a sensor to activate signaling pathways that determine cell fate. While the activation of these signaling pathways by translation elongation inhibitors has been well characterized, the impact of these inhibitors on mRNA dynamics remains unclear. Here we use TimeLapse sequencing to investigate how translational stress impacts mRNA dynamics in human cells. Our results reveal that a distinct group of transcripts is stabilized in response to the translation elongation inhibitor emetine. These stabilized mRNAs are short-lived at steady state and many of them encode C2H2 zinc finger proteins. The codon compositions of these stabilized transcripts are suboptimal compared to short-lived mRNAs that are not stabilized. Finally, we show that stabilization of these transcripts is independent of the signaling pathways activated by ribosome collisions, as well as of canonical ribosome quality control factors. Our data describe a group of transcripts whose degradation is particularly sensitive to the inhibition of translation elongation.

2024-10-01 | GSE264661 | GEO

Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [RNA-seq]

Project description:Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [RNA-seq]

| PRJNA744559 | ENA

Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [BiSulfite-seq]

Project description:Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [BiSulfite-seq]

| PRJNA744574 | ENA

Transcription profiling of Escherichia coli strain MG1655 response to NO released from NOC compounds

Project description:Escherichia coli strain MG1655 response to NO released from NOC compounds. Under contiuous steady state chemostat conditions, in chemically defined media.

2006-01-12 | E-MEXP-246 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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