Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Structural requirements for photo-induced RNA-protein cross-linking

ABSTRACT: Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the UV cross-linking behavior of in vitro reconstituted FOX1 RRM in complex with its cognate RNA sequence, the Fox binding element (FBE), (U)GCAUGU. The FBE heptanucleotide was subsequently mutated, and the impact on UV cross-linking and affinity investigated. Cross-linking was performed using irradiation under 254 nm light, relying on the inherent reactivity of ribonucleotides.

INSTRUMENT(S): Orbitrap Fusion Lumos, LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Christopher Sarnowski

LAB HEAD: Alexander Leitner

PROVIDER: PXD031381 | Pride | 2022-06-09

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	200625_LU2_csarnowski_AK301_01.raw	Raw
	200625_LU2_csarnowski_AK301_06.raw	Raw
	Fig1b.csv	Csv
	Fig1c.csv	Csv
	Fig2c_f.csv	Csv

Items per page:

1 - 5 of 88

Publications

Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes.

Knörlein Anna A Sarnowski Chris P CP de Vries Tebbe T Stoltz Moritz M Götze Michael M Aebersold Ruedi R Allain Frédéric H-T FH Leitner Alexander A Hall Jonathan J

Nature communications 20220517 1

Photo-induced cross-linking is a mainstay technique to characterize RNA-protein interactions. However, UV-induced cross-linking between RNA and proteins at "zero-distance" is poorly understood. Here, we investigate cross-linking of the RBFOX alternative splicing factor with its hepta-ribonucleotide binding element as a model system. We examine the influence of nucleobase, nucleotide position and amino acid composition using CLIR-MS technology (crosslinking-of-isotope-labelled-RNA-and-tandem-mass ...[more]

PMID: 35581222

Similar Datasets

Sensitive detection and structural characterisation of UV-induced cross-links in protein-ribonucleic acid complexes using stable isotope labelling and mass spectrometry

Project description: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-induced cross-links. Here we demonstrate protocol optimizations, and apply the enhanced protocol to a set of model protein-RNA complexes to better characterize the properties of UV-induced protein-RNA cross-links. We use these insights to study a non-canonical protein-RNA interaction between SF3A1 of the U2 snRNP and stem-loop 4 of the U1 snRNP, demonstrating that UV cross-linking and mass spectrometry is a reliable standalone data type for low resolution structural characterizations of protein-RNA interactions.

2023-09-06 | PXD029930 | Pride

RNxQuest: an extension to the xQuest pipeline enabling analysis of protein-RNA cross-linking/mass spectrometry data

2023-09-06 | PXD039754 | Pride

Sequence specific recognition of U1 snRNP stem-loop 4 by the ubiquitin-like domain of U2 snRNP protein SF3A1 and its RGG motif

Project description: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 isolation, and in broader context with components of the U1 snRNP. Cross-linking was performed using irradiation under 254 nm light, relying on the inherent reactivity of ribonucleotides.

2022-02-22 | PXD027189 | Pride

Hybrid structural modeling of protein-RNA complexes using crosslinking of segmentally isotope labeled RNA and tandem mass spectrometry

Project description: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 additionally applied to the U1 snRNP complex. Data from both complexes are included in this submission.

2017-03-27 | PXD005566 | Pride

Integrative structure determination of an 85-kilodalton PTBP1-IRES complex in solution reveals a strong compaction with pronounced conformational flexibility

Project description:Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the interaction between the four RNA recognition motifs (RRMs) of the protein PTBP1 with the internal ribosome entry site (IRES) of encephalomyocarditis virus (EMCV). These results are a reanalysis of PXD005566, with a broader parameter set.

2023-10-24 | PXD034894 | Pride

Structural insights into protein-RNA interactions within biomolecular condensates using UV cross-linking and mass spectrometry

Project description:UV-light-induced protein-RNA cross-linking followed by MS analysis was used to identify the interaction sites between protein and RNA in different phase-separated and non-phase separated states of complexes involving the following proteins: PTBP1, FUS, and SARS-CoV-2 nucleocapsid protein.

2024-03-06 | PXD046267 | Pride

An inhibitory segment within G-patch activators tunes Prp43-ATPase activity during ribosome assembly

Project description:Chemical cross-linking coupled to mass spectrometry using the amine-reactive DSS reagent was used to study the interactions between the RNA helicase Prp43 and its interactors, Pxr1 and Tma23, in Saccharomyces cerevisiae.

2024-10-02 | PXD047173 | Pride

Structural analysis of the native TREX complex from S. cerevisiae

Project description:Chemical cross-linking coupled to mass spectrometry was used to study the endogenously purified S. cerevisiae TREX complex. Cross-linking was performed using (a) bis(sulfosuccinimidyl) suberate (BS3) or (b) a combination of adipic dihydrazide (ADH) and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium (DMTMM) chloride.

2023-09-15 | PXD025843 | Pride

Comparison of OpenPepXL and xQuest on a Labeled Cross-Linking MS dataset

Project description:These data sets are part of a large study aimed at the comparison of experimental and computational workflows used in chemical cross-linking coupled to mass spectrometry. Bovine serum albumin (BSA) was used as a model protein. Two different cross-linking chemistries were used: disuccinimidyl suberate (DSS) and a combination of pimelic acid dihydrazide (PDH) and the coupling reagent, DMTMM. See related publication: Iacobucci et al., First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study, Analytical Chemistry, 91 (2019) 6953-6961, DOI: 10.1021/acs.analchem.9b00658 This project is a reanalysis of these datasets with the two Labeled Cross-Linking MS identification tools OpenPepXL and xQuest.

2020-10-20 | PXD014523 | Pride

Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry

Project description:Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by UV light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein–RNA and DNA interactions in one single experiment, we project that it will be possible to obtain completely new insights into chromatin and its regulation in the future.

2020-10-20 | PXD020290 | Pride