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ProteomicsHybrid structural modeling of protein-RNA complexes using crosslinking of segmentally isotope labeled RNA and tandem mass spectrometry
To study protein-RNA interactions at single amino acid and single nucleotide resolution we developed a new approach, termed cross-linking of segmentally isotope labeled RNA and tandem mass spectrometry (CLIR-MS/MS). The method was developed using the PTBP1-EMCV IRES complex as a model system and add...
ORGANISM(S): Homo sapiens (Human) 
2017-03-27 | PXD005566 | Pride
Photochemical cross-linking  protein-rna cross-linking  segmental isotope labeling of rna  clir-ms/ms  ribonucleoproteins  structural proteomics  polypyrimidine tract binding protein 1  u1 snrnp 
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
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
TranscriptomicsA Role for the RNA-Binding Protein MOS2 in MicroRNA Maturation in Arabidopsis
microRNAs (miRNAs) play important roles in the regulation of gene expression. In Arabidopsis, mature miRNAs are processed from primary miRNA transcripts (pri-miRNAs) by nuclear HYL1/SE/DCL1 complexes that form Dicing bodies (D-bodies). Here we report that a RNA-binding protein MOS2 bound to pri-miRN...
ORGANISM(S): Arabidopsis thaliana 
2012-10-27 | E-GEOD-41843 | biostudies-arrayexpress
ProteomicsSystem-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organisation and function of RNA-protein complexes
Production, function, and turnover of mRNA are orchestrated by multi-subunit machineries that play a central role in gene expression. Within these molecular machines, interactions with the target mRNA are mediated by RNA-binding proteins (RBPs), and the accuracy and dynamics of these RNA-protein int...
ORGANISM(S): Schizosaccharomyces pombe OY26 
2021-09-09 | PXD016741 | Pride
Rna exosome complex  rna interactome capture  rna-binding proteins  rna-protein crosslinking  ribonucleoprotein complexes 
TranscriptomicsIdentification of Neuronal RNA Targets of TDP-43-Containing Ribonucleoprotein Complexes
We identify the RNA targets of TAR DNA-binding protein 43 (TDP-43) from cortical neurons by RNA immunoprecipitation followed by deep sequencing (RIP-seq). We identify 4352 highly enriched RNA targets of TDP-43. We determined that the canonical TDP-43 binding site (TG)n was 55.1-fold enriched in our ...
ORGANISM(S): Rattus norvegicus 
2010-11-04 | E-GEOD-25032 | biostudies-arrayexpress
ProteomicsGlobal RNA-Protein Interactome purification screening identifies RRP1 in IL-1-stimulated BMDM cells
An “unbiased” approach that holds promise for isolating total protein-RNA complexes from whole cell samples without any labeling and identifying RBPs that lack classical RNA-binding domains (RBDs) or that bind different RNA classes is greatly needed. On the other hand, due to the scarcity of primary...
ORGANISM(S): Mus musculus (Mouse) 
2025-07-04 | PXD054800 | Pride
Rna-binding protein  primary macrophages  il-1 
TranscriptomicsPyrococcus furiosus crRNAs associated with Cmr, Csa and Cst CRISPR-Cas systems
CRISPR-Cas immune systems function to defend prokaryotes against potentially harmful mobile genetic elements including viruses and plasmids. The multiple CRISPR-Cas systems (Types I, II, III) each recognize and target destruction of foreign invader nucleic acids via structurally and functionally div...
ORGANISM(S): Pyrococcus furiosus 
2015-07-10 | E-GEOD-65781 | biostudies-arrayexpress
ProteomicsUnconventional RNA-binding proteins in mitosis
Ribonucleoprotein complexes are dynamic assemblies of RNA associated with RNA-binding proteins (RBPs), which can modulate the fate of the RNA molecules from transcription to degradation. Dysregulation of RBPs is linked to diseases such as cancer and neurological disorders, which motivated the develo...
ORGANISM(S): Homo sapiens (Human) 
2025-02-25 | PXD056233 | Pride
Rna-dependent protein-protein interactions Mitotic factors Rna-binding proteins 
ProteomicsA hybrid structural determination approach to investigate protein-RNA complexes of the nucleocapsid protein of SARS-CoV-2
UV-light-induced protein-RNA cross-linking followed by MS analysis was used to identify the interaction sites between the N-terminal (NTD) or C-terminal domain (CTD) of the SARS-CoV-2 nucleocapsid protein and the s2m element of the viral RNA.
ORGANISM(S): Severe acute respiratory syndrome coronavirus 2 
2023-03-13 | PXD037438 | Pride
Nucleocapsid Protein-rna cross-linking Uv cross-linking Protein-rna complexes Sars-cov-2 
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