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ProteomicsUtilization of Stability-based Proteomics for the Investigation of Structured RNA-protein Interactions
The stability of proteins from rates of oxidation (SPROX), thermal protein profiling (TPP) methods as well as triple helix pulldowns with LC-MS/MS readouts are used to identify the protein targets of three RNA ligands, the MALAT1 triple helix (TH), a viral stem loop (SL), and an unstructured RNA (Po...
ORGANISM(S): Homo sapiens (Human) 
2024-01-31 | PXD043878 | Pride
Thermodynamics Thermal denaturation Chemical denaturation Rna Rna-protein interactions Proteomics 
ProteomicsUCHL3 regulates subgenomic flaviviral RNA condensates to promote virus propagation
Flavivirus subgenomic RNAs (sfRNAs) antagonise antiviral defences, yet how sfRNAs are organised and maintained in cells remains poorly understood. Here we identify ubiquitin C-terminal hydrolase L3 (UCHL3) as a post-translational regulator of flavivirus sfRNA stability and function. Using a proximit...
ORGANISM(S): Homo sapiens (Human) 
2026-09-07 | PXD075983 | Pride
Dengue virus Flavivirus Biomolecular condensates Uchl3 Sfrna Zika virus Subgenomic rna 
ProteomicsIdentifying mTOR regulated RNA binding proteins
To investigate the RNA binding proteins that change following mTOR inhibition, HeLa cells were treated with and without 200nM Torin1 for an hour. Cells were the UV254 cross-linked, lysed and large scale whole cell oligo(dT) based pulldowns were performed with identification and quantification of pu...
ORGANISM(S): Homo sapiens (Human) 
2020-11-24 | PXD016705 | Pride
Nanoflow. Larp1 Mtor Synapt g2s Rna-binding proteins 
ProteomicsRNA pulldown-MS, Dlg4 RNA in mouse brain
Goal was to identify RNA-binding proteins with a preference for m6A-modified RNA using an RNA bait generated from a known m6A site in the Dlg4 (PSD-95) mRNA 3`-UTR. By comparison of differential enrichment between m6A-RNA pulldown fractions and A-RNA or no RNA fractions, we can identify m6A-binding ...
ORGANISM(S): Mus musculus (Mouse) 
2022-10-13 | PXD034159 | Pride
Pulldown M6a Rna Lc-ms/ms 
ProteomicsRNA pulldown-MS, Dlg4 RNA in mHippoE-2 cells
Goal was to identify RNA-binding proteins with a preference for m6A-modified RNA using an RNA bait generated from a known m6A site in the Dlg4 (PSD-95) mRNA 3`-UTR. By comparison of differential enrichment between m6A-RNA pulldown fractions and A-RNA or no RNA fractions, we can identify m6A-binding ...
ORGANISM(S): Mus musculus (Mouse) 
2022-10-13 | PXD034161 | Pride
Pulldown M6a Rna Lc-ms/ms 
ProteomicsA Circular RNA Controls Ribosomal RNA Maturation and Atherosclerosis in Humans
Circular RNAs (circRNAs) are broadly expressed in eukaryotic cells, but their role in human health and disease remains obscure. Here, we show that circular antisense non-coding RNA in the INK4 locus (circANRIL), which is transcribed at a locus of atherosclerotic cardiovascular disease on chromosome ...
ORGANISM(S): Homo sapiens (Human) 
2016-06-10 | PXD001769 | Pride
Circanril rna Pulse-silac Rna pulldowns Lc-ms/ms 
ProteomicsIdentifying cellular RNA-binding proteins during infection uncovers a role for MKRN2 in influenza mRNA trafficking.
Utilisation of RNA-binding proteins (RBPs) is an important aspect of post-transcriptional regulation of viral RNA. Viruses such as influenza A viruses (IAV) interact with RBPs to regulate processes including splicing, nuclear export and trafficking, while also encoding RBPs within their genomes, suc...
ORGANISM(S): Homo sapiens (Human) 
2024-04-16 | PXD048870 | Pride
Influenza mkrn2 rna-binding 
ProteomicsCCCP MS: Click and Chemical Cross-link Pulldowns of RNA interacting protein complexes for Mass Spectrometry-based identification
A workflow to isolate RNA binding proteins: Cells were labeled with an unnatural RNA base and cross linked with aldehyde. Cells were lysed and RNA protein complexes were immobilized to beads via click chemistry.
ORGANISM(S): Homo Sapiens (human) 
2021-05-11 | PXD019080 | JPOST Repository
ProteomicsThe interactome of flavin adenine dinucleotide (FAD) with RNA-binding proteins
We explored the interactome of flavin adenine dinucleotide (FAD) and the matrix of UV-immobilised FAD bound more than 3,000 proteins from SW-620 lysate. GO enrichment analysis showed that about 600 RNA-binding proteins were bound to FAD beads and, surprisingly, more than 40 proteins showed clear dos...
ORGANISM(S): Homo sapiens (Human) 
2022-10-06 | PXD036953 | Pride
Pum-rna Photo-immobilisation Fad Competition pulldown 
ProteomicsLENG8 mediates nuclear retention and degradation of misprocessed mRNAs and noncoding RNAs
Incompletely processed and misprocessed mRNAs as well as numerous noncoding RNAs are retained in the nucleus and often degraded, and defects in this quality control mechanism have been linked to various diseases, including cancer and neurodegeneration. However, the underlying mechanisms remain poorl...
ORGANISM(S): Homo sapiens (Human) 
2026-03-30 | PXD065356 | Pride
Misprocessed rnas Rna nuclear retention Rna degradation Leng8 
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