Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chemical nucleoside conversion-based measurement of RNA stability by targeted and untargeted mRNA 3´ end sequencing

ABSTRACT: Gene expression profiling by high-throughput sequencing determines changes in gene expression only at steady state but prevents our understanding of the underlying gene expression kinetics. Here, we describe a protocol that combines metabolic RNA labeling with thiol-specific chemical nucleoside conversion to determine the stability of polyadenylated RNA transcripts. And we provide a targeted mRNA 3 end library preparation protocol that enable to robustly determine the stability even of RNA transcripts that escape robust detection in untargeted libraries. The described methods enable cost-effective insights into the kinetics underlying steady-state gene expression in order to study the mechanisms underlying the regulation of gene expression at a transcript-specific and genomic scale.

ORGANISM(S): Mus musculus

PROVIDER: GSE118121 | GEO | 2019/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Scottish Vitamin D Intervention Study

Project description:AIMS To identify the underlying mechanism by which Vitamin D reduces colorectal cancer risk. OBJECTIVES To demonstrate the effects of vitamin D supplementation on serum vitamin D levels. To demonstrate dynamic changes in gene expression in response to vitamin D. To demonstrate the mechanism underlying the gene-environment interaction of vitamin D, susceptibility genetic variants (risk genes) and colorectal cancer.

| 2376099 | ecrin-mdr-crc

Saccharomyces cerevisiae

Project description:Gene Expression Kinetics

| PRJNA106355 | ENA

Chemical nucleoside conversion-based measurement of RNA stability by targeted and untargeted mRNA 3´ end sequencing

Project description:Chemical nucleoside conversion-based measurement of RNA stability by targeted and untargeted mRNA 3´ end sequencing

| PRJNA484507 | ENA

Expression data from regulatory T cells in mice

Project description:It is well accepted that the generation and functional stability of Treg cells stand as one dominant force to maintain immunological homeostasis during steady-state or under inflammatory conditions, as the primary Treg cell deficiency causes numerous types of autoimmunopathy, hypersensitivity or inflammation-induced carcinogenesis. We used microarrays to indentify the global programme of gene expression underlying regulatory mechanism and explore the differentially expressed genes during the process of immunology regulation.

2020-04-17 | GSE97927 | GEO

Transcription profiling of mouse cultured fibroblasts in response to the proinflammatory cytokine tumor necrosis factorA shows mRNA stability influences the temporal order of inflammatory gene induction

Project description:The inflammatory response plays out over time in a reproducible and organized manner after an initiating stimulus. Here we showed that the genes activated in cultured mouse fibroblasts in response to the proinflammatory cytokine tumor necrosis factorÂ can be divided roughly into three groups, each with different induction kinetics. Whereas differential transcription is important in determining the grouping of these genes, differential mRNA stability also exerted strong influence in some cases overriding that of transcriptional control elements on the temporal order of gene expression. mRNA transcripts expressed early after TNF stimulation have abundant AU-rich elements in their 3'-untranslated regions whereas those expressed later are contain fewer AU-rich sequences. Thus mRNA stability and transcriptional control, two intrinsic characteristics of genes, control the kinetics of proinflammatory cytokine-induced gene expression. Experiment Overall Design: The gene expression levels were monitored in the mouse embryonic cells stimulated with TNF for 0, 0.5h, 2h and 12 hours.

2009-01-18 | E-GEOD-14071 | biostudies-arrayexpress

mRNA stability influences the temporal order of inflammatory gene induction

Project description:The inflammatory response plays out over time in a reproducible and organized manner after an initiating stimulus. Here we showed that the genes activated in cultured mouse fibroblasts in response to the proinflammatory cytokine tumor necrosis factor can be divided roughly into three groups, each with different induction kinetics. Whereas differential transcription is important in determining the grouping of these genes, differential mRNA stability also exerted strong influence in some cases overriding that of transcriptional control elements on the temporal order of gene expression. mRNA transcripts expressed early after TNF stimulation have abundant AU-rich elements in their 3'-untranslated regions whereas those expressed later are contain fewer AU-rich sequences. Thus mRNA stability and transcriptional control, two intrinsic characteristics of genes, control the kinetics of proinflammatory cytokine-induced gene expression.

2009-01-07 | GSE14071 | GEO

Bulk-tissue RNA-sequencing paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen tissues from 4 post-mortem neuropathologically-confirmed control individuals ( anterior prefrontal cortex & cerebellar cortex Ã¢Â€Â“ 4 individuals, putamen- 3 individuals) .

Project description:Gaining insight into the genetic regulation of gene expression in human brain is key to the interpretation of genome-wide association studies for major neurological and neuropsychiatric diseases. Expression quantitative trait loci (eQTL) analyses have largely been used to achieve this, providing valuable insights into the genetic regulation of steady-state RNA in human brain, but not distinguishing between molecular processes regulating transcription and stability. RNA quantification within cellular fractions can disentangle these processes in cell types and tissues which are challenging to model in vitro. We investigated the underlying molecular processes driving the genetic regulation of gene expression specific to a cellular fraction using allele-specific expression (ASE). Applying ASE analysis to genomic and transcriptomic data from paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen tissues from 4 post-mortem neuropathologically-confirmed control human brains, we demonstrate that a significant proportion of genetic regulation of gene expression occurs post-transcriptionally in the cytoplasm, with genes undergoing this form of regulation more likely to be synaptic. These findings have implications for understanding the structure of gene expression regulation in human brain, and importantly the interpretation of rapidly growing single-nucleus brain RNA-sequencing and eQTL datasets, where cytoplasm-specific regulatory events could be missed.

| EGAS00001006380 | EGA

Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response

Project description:Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, miRNAs, and RNA-binding proteins. Here, we present Bru-Seq and BruChase-Seq to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at homeostasis and after exposure to the proinflammatory TNF. The inflammatory response in human cells involves rapid and dramatic changes in gene expression, and the Bru-Seq and BruChase-Seq techniques revealed a coordinated and complex regulation of gene expression both at the transcriptional and posttranscriptional levels. The combinatory analysis of both RNA synthesis and stability using Bru-Seq and BruChase-Seq allows for a much deeper understanding of mechanisms of gene regulation than afforded by the analysis of steadystate total RNA and should be useful in many biological settings. Analysis of the effect of TNF exposure in nascent gene expression and in transcript stability

2013-01-29 | E-GEOD-43440 | biostudies-arrayexpress

Ultra short and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

Project description:RNA synthesis and decay rates determine the steady-state levels of cellular RNAs. Metabolic tagging of newly transcribed RNA by 4-thiouridine (4sU) can reveal the relative contributions of RNA synthesis and decay rates. The kinetics of RNA processing, however, so far remained unresolved. Here, we show that ultra-short 4sU-tagging not only provides snap-shot pictures of eukaryotic gene expression but, when combined with progressive 4sU-tagging and RNA-seq, reveals global RNA processing kinetics at nucleotide resolution. Using this method, we identified classes of rapidly and slowly spliced/degraded introns. Interestingly, each class of splicing kinetics was characterized by a distinct association with intron length, gene length and splice site strength. For a large group of introns, we also observed long lasting retention in the primary transcript, but efficient secondary splicing or degradation at later time points. Finally, we show that processing of most, but not all small nucleolar (sno)RNA-containing introns is remarkably inefficient with the majority of introns being spliced and degraded rather than processed into mature snoRNAs. In summary, our study yields unparalleled insights into the kinetics of RNA processing and provides the tools to study molecular mechanisms of RNA processing and their contribution to the regulation of gene expression.

2012-04-26 | GSE31653 | GEO

The change of mRNA stability upon T cell activation

Project description:T cell activation is a well-established model for studying cellular responses to exogenous stimulation. In this study, we performed BruChase-Seq to experimentally monitor the expression dynamics of nascent transcripts in resting and activated CD4+ T cells, and applied computational modeling to investigate the impact of IR on the kinetics of mRNA degradation. As expected, intron retained transcripts are considerably less stable than spliced transcripts. In addition, the decrease in the steady-state IR level in activated CD4+ T cells are in part due to increased splicing efficiency and further stabilization of spliced transcripts. We propose that coordination between splicing regulation and mRNA stability may provide a novel paradigm to achieve spatiotemporal control of gene expression during T cell activation. We also found the mRNA stability change is not due to the 3’UTR-isoform choice but may be regulated by the RBP for example the LARP4 is the most significant binding protein in 3’ UTR of the β1-decreased genes. Furthermore, the mRNAs of the activated CD4+ T cells in LARP4 Knock-out (KO) mice showed the decreased stability and comparable transcriptional level for some genes including the NFkB1 and PSMD7 when comparing to the wild-type (WT) mice, resulting in the down-regulation of these genes. Finally, the LARP4 KO down-regulated NFkB1 target genes such as IL2 and IFNG upon CD4+ T cell activation, which is critical for the T cell proliferation and function.

2020-07-21 | GSE113730 | GEO

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