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ProteomicsUV-inducible crosslinking IP-MS to elucidate the role of nuclear Hsp104 during quiescence in Saccharomyces cerevisiae
In this study, we utilize high-content microscopy screening and quantitative proteomics to establish a function of nuclear Hsp104 during aging. We find that the cytosolic-nuclear partitioning of Hsp104 is critical to maintain nuclear proteostasis in quiescent cells. Whereas high global translation r...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2024-01-12 | PXD043093 | Pride
P-benzoyl-l-phenylalanine Yeast Quiescence Uv-inducible crosslinking Nuclear protein quality control Ip-ms Ageing Co-immunoprecipitation Lc-ms/ms Translation Hsp104 Proteomics Disaggregation 
OtherPhotoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of the RNA-binding protein (RBP) RBM4 in KBM-7 derived near-haploid human cell line, HAP1.
We hypothesized that RBM4 regulates HERVs by directly binding to their transcripts. To test this possibility, we performed photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP). We performed four independent PAR-CLIP replicates of our own using HAP1 cells stably ex...
ORGANISM(S): Homo sapiens 
2020-09-03 | GSE147895 | GEO
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 
GenomicsPhotoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of the RNA-binding protein (RBP) RBM4 in KBM-7 derived near-haploid human cell line, HAP1.
Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of the RNA-binding protein (RBP) RBM4 in KBM-7 derived near-haploid human cell line, HAP1.
PRJNA622499 | ENA
ProteomicsSystematic discovery of UFM1 receptors reveals a regulatory module in DNA repair directing non-homologous end-joining
As the most recently identified UBL, UFM1 is garnering increasing attention for its roles beyond its canonical functions at the endoplasmic reticulum. To address the challenge of defining UFM1 substrate-receptor relationships, we develop a fully functional, photo-crosslinkable UFM1 probe for recepto...
ORGANISM(S): Homo sapiens (Human) 
2026-06-25 | PXD069136 | Pride
Ufm1  ubiquitin-like proteins (ubls)  dna repair  dna double-strand breaks (dsbs)  non-homologous end-joining (nhej)  xrcc4  genetic code expansion  photo-crosslinking  proximity labelling 
ProteomicsProbing protein dynamics in inducible nitric oxide synthase by photoactivated cross-linking mass spectrometry
Quantitative XL-MS using sulfo-SDA, a heterobifunctional cross-linker with ultrafast broad residue reactivity upon UV-triggered carbene formation, to study E546N mutation-dependent decreases in specific inter-subunit FMN–heme cross-links in human inducible NOS (iNOS).
ORGANISM(S): Homo sapiens (Human) 
2026-09-09 | PXD080124 | Pride
Photoactivated Xl-ms Nos 
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 
TranscriptomicsHigh-throughput identification of miRNA targets using CLASH (crosslinking, ligation and sequencing of hybrids)
Purpose: Identification of miRNA-mRNA interactions in human cells. Method: We used the CLASH technique with PTH-tagged AGO1 protein as a bait. Results: In 6 experiments we identified more than 18,000 miRNA-mRNA interactions in human HEK293 cells, corresponding to targets of 399 miRNAs. Conclusions:...
ORGANISM(S): Saccharomyces cerevisiae 
2013-08-30 | E-GEOD-50452 | biostudies-arrayexpress
UnknownDisplacement of the transcription factor B reader domain during transcription initiation.
Not available
S-EPMC6212726 | biostudies-literature
TranscriptomicshnRNP A1 iCLIP
This experiment identifies hnRNP A1 binding sites transcriptome-wide in Hela cells. HeLa cells with inducible expression of T7-tagged hnRNP A1 were grown to approximately 90% confluence and then subject to iCLIP analysis (following the protocol from Huppertz et al. 2014 (iCLIP: protein-RNA interact...
ORGANISM(S): Homo sapiens 
2016-06-23 | E-MTAB-3612 | biostudies-arrayexpress
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