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MetabolomicsN6-methyladenosine modification is not a general trait of positive-sense RNA viral genomes

Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-seq, an antibody-dependent technique with...

2024-01-25 | MTBLS6978 | MetaboLights
ProteomicsLocal RNA translation controls cell migration and Rab GTPase function
Numerous RNAs exhibit specific distribution patterns in mammalian cells. However, the functional and mechanistic consequences are relatively unknown. We investigate here the functional role of RNA localization at cellular protrusions of mesenchymal migrating cells, using as a model the RAB13 RNA, wh...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-08-01 | MSV000085883 | MassIVE
ProteomicsSubCellBarcode: Scalable proteome-wide mapping of protein localization and relocalization
We have devised a simple and robust LC-MS/MS compatible protocol for subcellular protein localization studies. Here, we combine it with in depth proteome profiling and utilize the resulting dataset to predict the subcellular localization of more than 12000 proteins in 5 human cancer cell lines. The ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2021-02-17 | MSV000086899 | MassIVE
TranscriptomicsLooking for mitochondrial associated RNA
We investigated the peripheral mitochondrial localization of nuclear-encoded mRNAs (MLR) in various conditions in which translation was inhibited or the mRNA binding protein context altered (Delta puf3). We used cell fractionation protocols together with microarray to assess the distribution of mRNA...
ORGANISM(S): Saccharomyces cerevisiae 
2008-06-01 | E-GEOD-9393 | biostudies-arrayexpress
ProteomicsSimultaneous proteome localization and turnover analysis reveals spatiotemporal coordinations of unfolded protein response
The functionality of proteins is dependent on their spatial and temporal distributions, neither of which is directly measured by static protein abundance. Here we report a mass spectrometry-based proteomics workflow and data analysis pipeline, named Simultaneous Proteome Localization and Turnover (...
ORGANISM(S): Homo Sapiens (human) 
2022-12-31 | PXD038054 | JPOST Repository
GenomicsDistinct factors control histone variant H3.3 localization at specific genomic regions
The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem (ES) cells and neuronal precursor cells. Genome-w...
ORGANISM(S): Mus musculus 
2010-03-04 | E-GEOD-16893 | biostudies-arrayexpress
GenomicsAltered Subcellular Localization of Transcription Factor TEAD4 Regulates First Mammalian Cell Lineage Commitment
In the preimplantation mouse embryo TEAD4 is critical to establishing the trophectoderm (TE)-specific transcriptional program and segregating TE from the inner cell mass (ICM). However, TEAD4 is expressed both in the TE and the ICM. Thus, differential function of TEAD4 rather than expression itself ...
ORGANISM(S): Mus musculus 
2012-04-18 | E-GEOD-37350 | biostudies-arrayexpress
ProteomicsIdentification of RNA-binding proteins interacting with axonal localization elements
Here, we used axonal RNA localization motifs as baits coupled with mass spectrometry (MS) to identify the RNA binding proteins that bind to Nrn1 (also called Cortical Plasticity Gene 15), Hmgb1 (also called Amphoterin), Actb, and Gap43 mRNA localization motifs.
ORGANISM(S): Rattus Norvegicus (ncbitaxon:10116) 
2018-01-10 | MSV000081910 | MassIVE
ProteomicsA massively parallel reporter assay reveals novel features and players of RNA localization in neurons
This experiment aims to identify the RNA-binding proteome that is pulled-down from a cellular lysate with biotinylated RNA probes.
ORGANISM(S): Mus musculus (Mouse) 
2021-04-30 | PXD025492 | Pride
Mpra Pull-down Rna localization 
GenomicsRNA localization to stress granules
RNA localization to stress granules
PRJNA875210 | ENA
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