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ProteomicsTargeted RNase H-mediated Extraction of crosslinked RBPs (TREX) for assessing U1 RNA interactome
We used Targeted RNase H-mediated Extraction of crosslinked RBPs (TREX)to assess the endogenous binding partners of U1 small nuclear RNA (U1 snRNA) in human HCT116 cells. Extracted proteins from U1 digested and control cells (5 replicate per condition) were compared, using label-free (LFQ) Quantitat...
ORGANISM(S): Homo sapiens (Human) 
2023-12-27 | PXD044643 | Pride
Trex  rbp  rna interactome  lc-ms/ms  quantitative proteomics 
ProteomicsCAPRI RNA binding proteins and domains in Drosophila and Humans
In the current work, we present a comprehensive coverage of the RNA-binding protein (RBP) interactome of Drosophila at four levels of resolution. The highest level tackled in our study represents the RNA-protein complexes, which we address by combining formaldehyde crosslinking of Drosophila S2 cell...
ORGANISM(S): Homo sapiens (Human) Drosophila melanogaster (Fruit fly) 
2019-07-02 | PXD013338 | Pride
Rna crosslinked peptides Rna protein interaction 
TranscriptomicsTranscriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data
We applied 4-thiouridine to cultured cells expressing the FLAG/HA-tagged RNA-binding proteins (RBPs) followed by UV 365 nm irradiation. The crosslinked RNA-protein complexes were isolated by immunoprecipitation, and the covalently bound RNA was partially digested with RNase T1 and radiolabeled. The ...
ORGANISM(S): Homo sapiens 
2010-05-21 | E-GEOD-21918 | biostudies-arrayexpress
ProteomicsUV-crosslinking mapping of LARP6 interaction sites with RNA
To map the regions of LARP6 that interacts directly with RNA, we developed a mass spectrometry-based approach termed IP-OOPS (Immunoprecipitation coupled with Orthogonal Organic Phase Separation. This approach combines the isolation of UV-C crosslinked RNA–protein adducts via Orthogonal Organic Phas...
ORGANISM(S): Homo sapiens (Human) 
2026-01-22 | PXD064029 | Pride
Lc-ms/ms  rna-protein interactions  organic phase separation  rna crosslinking 
ProteomicsUnbiased characterization and systematic profiling of metabolically labeled RNA-binding sites
Here we introduce pRBS-ID, an amenable platform that enables robust profiling of PAR-crosslinked RBSs. Using tandem mass spectrometry (MS/MS) approaches, we unbiasedly characterize the PAR adducts on peptides, to develop an optimal MS/MS search pipeline that enables robust identification and quantif...
ORGANISM(S): Homo sapiens (Human) 
2021-11-02 | PXD023401 | Pride
Human Lc-ms/ms 
ProteomicsDirect Interactions of RNA Polymerase with Ribosomes and Ribosomal Subunits in E. Coli
The interactions between RNA polymerase and ribosomes are critical for the coordination of transcription with translation. We report that RNA polymerase directly binds ribosomes and isolated large and small ribosomal subunits.
ORGANISM(S): Escherichia coli 
2017-08-28 | PXD006717 | Pride
Ribosomes Mass spectrometry E. coli Rna polymerase 
UnknownNovel miR-122 delivery system based on MS2 virus like particle surface displaying cell-penetrating peptide TAT for hepatocellular carcinoma.
Not available
S-EPMC5312320 | biostudies-literature
ProteomicsTargeted RNase H-mediated Extraction of crosslinked RBPs (TREX) for assessing region-specific NORAD lncRNA interactome
We used Targeted RNase H-mediated Extraction of crosslinked RBPs (TREX)to assess the endogenous binding partners of the ND4 segment of NORAD long noncoding RNA (lncRNA) in human HCT116 cells. Extracted proteins from RNase H digested and control cells (4 replicate per region per condition) were compa...
ORGANISM(S): Homo sapiens (Human) 
2023-12-27 | PXD045385 | Pride
Norad  nd4  lncrna  trex  rbp  rna interactome  lc-ms/ms  quantitative proteomics 
ProteomicsNpl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA
RNA-binding proteins (RBPs) control every RNA metabolic process by multiple protein-RNA and protein-protein interactions. Their roles have largely been analyzed by crude mutations, which abrogate several functions at once and likely impact the structural integrity of the large mRNP assemblies, these...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-03-11 | PXD035153 | Pride
Rna-binding sites Npl3 Sr-like protein Mrnp assembly Structure Xl-ms Rna-binding proteins Nmr Mrna Gene expression 
UnknownThe signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome.
Not available
S-EPMC1370422 | biostudies-literature
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