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MetabolomicsA multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6 (NMR assay)

Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that capt...

2020-02-14 | MTBLS1320 | MetaboLights
MetabolomicsSimultaneous Membrane and RNA Binding by Tick-Borne Encephalitis Virus Capsid Protein

Tick-borne encephalitis virus is an enveloped, pathogenic, RNA virus in the family Flaviviridae, genus Flavivirus. Viral particles are formed when the nucleocapsid, consisting of an RNA genome and multiple copies of the capsid protein, buds through the endoplasmic reticulum membrane and acquires ...

2023-01-06 | MTBLS6076 | MetaboLights
ProteomicsDNA binding reorganizes the intrinsically disordered C-terminal region of PSC in Drosophila PRC1
Polycomb Group (PcG) proteins regulate gene expression by modifying chromatin. A key PcG complex, PRC1, has two activities: a ubiquitin ligase activity for histone H2A, and a chromatin compacting/nucleosome bridging activity that can inhibit transcription and chromatin remodeling. In Drosophila, the...
ORGANISM(S): Drosophila Melanogaster (ncbitaxon:7227) 
2020-05-15 | MSV000085418 | MassIVE
ProteomicsNucleosome binding by the pioneer transcription factor OCT4
The nucleosome is a fundamental unit of chromatin in eukaryotes, and generally prevents the binding of transcription factors to genomic DNA. Pioneer transcription factors overcome the nucleosome barrier, and bind their target DNA sequences in chromatin. OCT4 is a representative pioneer transcription...
ORGANISM(S): Homo Sapiens (human) 
2020-05-13 | PXD019160 | JPOST Repository
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
TranscriptomicsA modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity
We examine the use of high-throughput sequencing on binding sites recovered using a bacterial one-hybrid (B1H) system and find that improved models of transcription factor (TF) binding specificity can be obtained compared to standard methods of sequencing a small subset of the selected clones. We ca...
ORGANISM(S): synthetic construct 
2011-04-28 | E-GEOD-26767 | 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
ProteomicsIdentification of cellular proteins binding to the 3’UTR of Programmed Cell Death 4 mRNA
The aim of the project is to identify RNA-binding proteins (RBPs) that interact with the 3’ untranslated region (3’UTR) of the programmed cell death 4 (PDCD4) mRNA. PDCD4 is an inflammatory tumor suppressor gene. The translation of PDCD4 mRNA is regulated by multiple RBPs. The aim is to identify RBP...
ORGANISM(S): Homo sapiens (Human) 
2020-12-11 | PXD017376 | Pride
Mass spectrometry 3’ untranslated region Rna-protein interaction Programmed cell death 4 Rna-binding protein 
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
GenomicsTranscriptome-wide mapping of RNA binding sites of the RNA-binding protein Unkempt using iCLIP-seq
iCLIP experiments tomap the RNA binding sites of the RNA-binding protein Unkempt across the transcriptome in SH-SY5Y cells, HeLa cells with ectopic Unk expression and mouse E15 embryonic brain samples. Expression of Unk is normally largely restricted to the nervous system. We therefore mapped the bi...
ORGANISM(S): Homo sapiens 
2015-03-09 | E-MTAB-2279 | biostudies-arrayexpress
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