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MetabolomicsFate and PPARγ and STATs-driven effects of the mitochondrial complex I inhibitor tebufenpyrad in liver cells revealed with multi-omics.
The biological effects of the pesticide and mitochondrial complex I inhibitor tebufenpyrad (TEBU) on liver cells were investigated by combining proteomics and metabolomics. Both cell culture media and cellular lysates were analyzed in dose-response and kinetic experiments on the HepaRG cell line. Re...
2024-02-07 | MTBLS4063 | MetaboLights
MetabolomicsPrediction of complex phenotypes using the Drosophila melanogaster metabolome
Understanding the genotype-phenotype map and how variation at different levels of biological organization is associated are central topics in modern biology. Fast developments in sequencing technologies and other molecular omic tools enable researchers to obtain detailed information on variation at ...
2021-08-05 | MTBLS2060 | MetaboLights
MetabolomicsAccumulation of the coumarin scopolin under abiotic stress conditions is mediated by the Arabidopsis thaliana THO/TREX complex
Secondary metabolites are involved in the plant stress response. Among these are scopolin and its active form scopoletin, which are coumarin derivatives associated with reactive oxygen species scavenging and pathogen defence. Here we show that in Arabidopsis thaliana, scopolin accumulation can be in...
2018-02-05 | MTBLS389 | MetaboLights
ProteomicsEnzymatic Site-specific Biotinylation Enables Analysis of RNA-protein Interactions and Enrichment of Cellular RNA
The importance of RNA in regulating cellular processes has generated tremendous interest in methods to reliably characterize RNAs and their interactions within cells. Existing methodologies rely on noncovalent interactions to facilitate RNA affinity purification, hindering the purification of less a...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-03-13 | MSV000085100 | MassIVE
GenomicsMediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA
CCCTC-binding factor (CTCF) is a DNA-binding protein that plays important roles in chromatin organization, though the mechanism by which CTCF carries out these functions is not fully understood. Recent studies show that CTCF recruits the cohesin complex to insulator sites and that cohesin is require...
ORGANISM(S): Homo sapiens 
2010-11-16 | E-GEOD-24126 | biostudies-arrayexpress
ProteomicsYBX3 is a versatile RNA-binding protein that controls amino acid import by regulating SLC mRNA abundance
Summary: Amino acids (AA) support protein synthesis, and thus cell growth and proliferation. Specialized transporters mediate AA exchange across membranes and their regulation is critical for AA homeostasis. Here, we report that the DNA- and RNA-binding protein YBX3 regulates the expression of AA t...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-11-06 | MSV000083108 | MassIVE
TranscriptomicsRNA-protein interaction screening for SNORD50A and SNORD50B
Putative RNA-protein interactions with selected snoRNAs were screened using labaled RNA hybridized to a human protein microarray snoRNAs SNORD50A and SNORD50B were in vitro transcribed, labeled with Cy5 and independently hybridized on human protein microarrays. The labeling process was optimized in ...
ORGANISM(S): Homo sapiens 
2015-11-23 | E-GEOD-51817 | biostudies-arrayexpress
TranscriptomicsGlobal analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus
Post-transcriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure, and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of RNAs in the nucleus has yet to be compiled for any or...
ORGANISM(S): Arabidopsis thaliana 
2014-12-16 | E-GEOD-58974 | biostudies-arrayexpress
ProteomicsThe concept of "RNA dependence" - Proteome-wide and quantitative identification of protein interactions dependent on RNA
The general role of RNA in the cell beyond protein biosynthesis is only beginning to emerge with little knowledge about the structural or organizational functions of RNA. In turn, functional non-coding RNAs (ncRNAs) are often identified by their regulation or impact on cellular phenotypes. However, ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-06-13 | MSV000082468 | MassIVE
GenomicsPolycomb Protein Ezh1 Promotes RNA Polymerase II Elongation
Polycomb group (PcG) proteins initiate the formation of repressed chromatin domains and regulate developmental gene expression. A mammalian PcG protein, Enhancer of Zeste homolog 2 (Ezh2), triggers transcriptional repression by catalyzing the addition of methyl groups onto lysine-27 of histone H3 (...
ORGANISM(S): Mus musculus 
2011-11-23 | E-GEOD-25549 | biostudies-arrayexpress
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