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TranscriptomicsGlobal analysis of mRNA decay intermediates in Saccharomyces cerevisiae
The general pathways of eukaryotic mRNA decay occur via deadenylation followed by 3’ to 5’ degradation or decapping, although some endonuclease sites have been identified in metazoan mRNAs. To determine the role of endonucleases in mRNA degradation in Saccharomyces cerevisiae, we mapped 5’ monophosp...
ORGANISM(S): Saccharomyces cerevisiae 
2012-06-17 | E-GEOD-33712 | biostudies-arrayexpress
TranscriptomicsRNAi knock down of known nonsense-mediated mRNA decay (NMD) factors in Drosophila cells
All eukaryotes studied to date have the capacity to detect and degrade mRNAs harboring premature translation termination codons (PTCs) in a process called nonsense-mediated mRNA decay (NMD) (reviewed in Wagner E & Lykke-Andersen J, 2002). This surveillance system allows the cell to prevent the expre...
ORGANISM(S): Drosophila melanogaster 
2005-11-01 | E-MEXP-202 | biostudies-arrayexpress
TranscriptomicsNET-seq of S. cerevisiae cells after knocking-out genes encoding various mRNA decay factors
NET-seq was performed on yeast strains carrying deletions of mRNA decay factors (plus a control) in order to assess the effect of their deletion on RNA polymerase II occupancy at genetic loci. This is in pursuit of understanding the process of mRNA buffering which links mRNA synthesis and decay.
ORGANISM(S): Saccharomyces cerevisiae 
2020-02-08 | E-MTAB-8749 | biostudies-arrayexpress
ProteomicsThe Parkinson's disease protein alpha-synuclein is a direct modulator of Processing-bodies and mRNA stability
Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR,Carr SA, de Jager P, Myers CL, Lindquist S, Greenmyre TJ, Bartel DP, Feany MB, Sunyaev S, Chung CY and Khurana V. Alp...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-03-09 | MSV000089026 | MassIVE
TranscriptomicsPervasive TTP binding but selective target mRNA destabilization in the macrophage transcriptome [RNA-Seq_2]
Precise control of mRNA decay is fundamental for robust yet not exaggerated inflammatory responses to pathogens. Parameters determining the specificity and extent of mRNA degradation within the entire inflammation-associated transcriptome remain incompletely understood. Using transcriptome-wide high...
ORGANISM(S): Mus musculus 
2016-05-17 | E-GEOD-78209 | biostudies-arrayexpress
TranscriptomicsMeasurements of mRNA abundance and decay for two strains 211 (wt) and 212 (mutant)
For each strain two time courses for mRNA abundance: Oxidative and MMS and two time courses for decay: reference decay and following oxidative stress We used Affymetrix microarrays to quantify changes in mRNA abundance following oxidative stress and DNA damage stress and also decay following transcr...
ORGANISM(S): Saccharomyces cerevisiae 
2011-07-29 | E-GEOD-26829 | biostudies-arrayexpress
TranscriptomicsRibosome profiling of early zebrafish embryos -- miRNA-mediated regulation during embryogenesis causes translational repression before mRNA decay
MicroRNAs regulate gene expression through deadenylation, repression and mRNA decay. However, the contribution of each mechanism in non-steady-state situations remains unclear. We monitored the impact of miR-430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature...
ORGANISM(S): Danio rerio 
2012-03-15 | E-GEOD-34743 | biostudies-arrayexpress
TranscriptomicsRoles of mRNA decay in liver development
mRNA decay machineries play important roles in various biological events. Among them, Cnot deadenylase complex has a critical function to trigger mRNA decay. To understand roles of the complex in liver development, we compare RNA expression between control and Cnot complex-deficient liver.
ORGANISM(S): Mus musculus 
2019-02-01 | E-MTAB-7182 | biostudies-arrayexpress
TranscriptomicsExamination of mRNA decay rate in mouse embryonic fibroblasts
The CCR4-NOT dedadenylase complex is essential for mRNA decay and various biological events.To understand roles of the complex in mouse embryonic fibroblasts, we compared mRNA half-lives between control and Cnot complex-deficient mouse embryonic fibroblasts
ORGANISM(S): Mus musculus 
2020-01-29 | E-MTAB-8287 | biostudies-arrayexpress
TranscriptomicsQuality control of transcription start site selection by Nonsense-Mediated-mRNA Decay
Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA quality-control pathway targeting transcripts such as messenger RNAs harboring premature stop-codons or short upstream open reading frame (uORFs). Our transcription start sites (TSSs) analysis of Saccharomyces cerevisiae cells deficie...
ORGANISM(S): Saccharomyces cerevisiae BY4741 
2015-04-24 | E-GEOD-64139 | biostudies-arrayexpress
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