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ProteomicsDithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions
In the present paper, we introduce dithiothreitol (DTT) as a potent protein-RNA cross-linker. To prove this three model systems, a) a small synthetic peptide from smB'/B protein incubated with U1snRNA oligonucleotide, b) in vitro reconstituted 15.5K protein with U4 snRNA oligonucleotide and c) nativ...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2022-03-01 | PXD002392 | Pride
Dtt Protein-rna cross-links 
ProteomicsIntensity and retention time prediction improves the rescoring of protein-nucleic acid cross-links
Rescoring of protein-RNA cross-links using retention time and intensity prediction.
ORGANISM(S): Escherichia coli 
2025-11-24 | PXD048145 | Pride
Lc-msms Protein-rna cross-links Bottom-up proteaomics 
ProteomicsSensitive detection and structural characterisation of UV-induced cross-links in protein-ribonucleic acid complexes using stable isotope labelling and mass spectrometry
The recently introduced cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) technique enables protein-RNA cross-links to be used as precisely localized distance restraints in de novo structural modelling, but little is known about the structural characteristics of UV-induc...
ORGANISM(S): Homo sapiens (Human) 
2023-09-06 | PXD029930 | Pride
Uv cross-linking  mbnl1  fox1  ptbp1  sf3a1  u1  u2  cross-linking  xl-ms  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms 
TranscriptomicsAnalysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are the most frequently used methods to study protein-RNA interactions in the intact cells and tissues, but their relative advantages or inherent biases have not been evaluated. To benchmark CLIP and iC...
ORGANISM(S): Mus musculus 
2012-07-20 | E-MTAB-1008 | biostudies-arrayexpress
ProteomicsRNxQuest: an extension to the xQuest pipeline enabling analysis of protein-RNA cross-linking/mass spectrometry data
The recently introduced cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) technique enables protein-RNA cross-links to be used as precisely localized distance restraints in de novo structural modelling. The novel data type requires a bespoke data analysis approach. The n...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2023-09-06 | PXD039754 | Pride
Uv cross-linking  mbnl1  fox1  ptbp1  bsa  cross-linking  xl-ms  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms 
ProteomicsDithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions
In the present paper, we introduce dithiothreitol (DTT) as a potent protein-RNA cross-linker. To prove this three model systems, a) a small synthetic peptide from smB'/B protein incubated with U1snRNA oligonucleotide, b) in vitro reconstituted 15.5K protein with U4 snRNA oligonucleotide and c) nativ...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2015-10-13 | PXD002656 | Pride
Dtt 
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
ProteomicsReconstitution of mammalian Cleavage Factor II
Cleavage factor II (CF II) is a poorly characterized component of the multi-protein complex catalyzing 3' cleavage and polyadenylation of mammalian mRNA precursors. We have reconstituted CF II as a heterodimer of hPcf11 and hClp1. The heterodimer is active in partially reconstituted cleavage reactio...
ORGANISM(S): Homo sapiens (Human) 
2020-05-26 | PXD010177 | Pride
Human Rna processing Dsbu 
ProteomicsSequence specific recognition of U1 snRNP stem-loop 4 by the ubiquitin-like domain of U2 snRNP protein SF3A1 and its RGG motif
Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the interaction between the ubiquitin-like domain (UBL) of the protein SF3A1, a component of the U2 snRNP, with stem-loop 4 RNA (SL4) from the U1 snRNP. The complex was cross-linked and analysed both in ...
ORGANISM(S): Homo sapiens (Human) 
2022-02-22 | PXD027189 | Pride
Uv cross-linking  sf3a1  u1  u2  snrnp  splicing  spliceosome  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms 
UnknownPinpointing RNA-Protein Cross-Links with Site-Specific Stable Isotope-Labeled Oligonucleotides.
Not available
S-EPMC4697197 | biostudies-literature
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