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Cited by 12Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsRNA and protein synthesis mechanisms

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Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid–protein interaction sites by mass spectrometry

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Welp, Luisa M, Wulf, Alexander, Chernev, Aleksandar, Horokhovskyi, Yehor, Moshkovskii, Sergei, Dybkov, Olexandr, Neumann, Piotr, Pašen, Martin, Siraj, Arslan, Raabe, Monika, Göthert, Henri, Walshe, James L, Infante, Deliana A, de A.P. Schwarzer, Ana C, Dickmanns, Achim, Johannsson, Sven, Schmitzová, Jana, Wohlgemuth, Ingo, Netz, Eugen, He, Yi, Fritzemeier, Kai, Delanghe, Bernard, Viner, Rosa, Vos, Seychelle M, Oberbeckmann, Elisa, Bohnsack, Katherine E, Bohnsack, Markus T, Cramer, Patrick, Ficner, Ralf, Kohlbacher, Oliver, Liepe, Juliane, Sachsenberg, Timo, Urlaub, Henning·2025·Nucleic Acids Research
DOI 10.1093/nar/gkaf727PMC PMC12359043

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Abstract

Ultraviolet (UV) crosslinking with mass spectrometry (XL-MS) has been established for identifying RNA- and DNA-binding proteins along with their domains and amino acids involved. Here, we explore chemical XL-MS for RNA–protein, DNA–protein, and nucleotide–protein complexes in vitro and in vivo. We introduce a specialized nucleotide–protein-crosslink search engine, NuXL, for robust and fast identification of such crosslinks at amino acid resolution. Chemical XL-MS complements UV XL-MS by generating different crosslink species, increasing crosslinked protein yields in vivo almost four-fold, and thus it expands the structural information accessible via XL-MS. Our workflow facilitates integrative structural modelling of nucleic acid–protein complexes and adds spatial information to the described RNA-binding properties of enzymes, for which crosslinking sites are often observed close to their cofactor-binding domains. In vivo UV and chemical XL-MS data from E. coli cells analysed by NuXL establish a comprehensive nucleic acid–protein crosslink inventory with crosslink sites at amino acid level for >1500 proteins. Our new workflow combined with the dedicated NuXL search engine identified RNA crosslinks that cover most RNA-binding proteins, with DNA and RNA crosslinks detected in transcriptional repressors and activators.

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Metadata

Authors
Welp, L. M., Wulf, A., Chernev, A., Horokhovskyi, Y., Moshkovskii, S., Dybkov, O., Neumann, P., Pašen, M., Siraj, A., Raabe, M., Göthert, H., Walshe, J. L., Infante, D. A., de A.P. Schwarzer, A. C., Dickmanns, A., Johannsson, S., Schmitzová, J., Wohlgemuth, I., Netz, E., He, Y., Fritzemeier, K., Delanghe, B., Viner, R., Vos, S. M., Oberbeckmann, E., Bohnsack, K. E., Bohnsack, M. T., Cramer, P., Ficner, R., Kohlbacher, O., Liepe, J., Sachsenberg, T., & Urlaub, H.
Affiliations
  • Universitätsmedizin Göttingen (DE)
  • Max Planck Institute for Multidisciplinary Sciences (DE)
  • University of Göttingen (DE)
  • University of Tübingen (DE)
  • University Medical Center Göttingen Department of Molecular Biology, , Göttingen 37077 ,
  • Thermo Fisher Scientific , San Jose , CA  95134 ,
  • Thermo Fisher Scientific , Bremen  28199 ,
  • Howard Hughes Medical Institute (US)
  • Universitätsklinikum Tübingen (DE)
Corresponding author
  • Kohlbacher, Oliver
  • Liepe, Juliane
  • Sachsenberg, Timo
  • Urlaub, Henning
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2025-08-11
Volume
53
Issue
15
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkaf727
PMC
PMC12359043
OpenAlex
W4413309406
Cited by
12
References
3
Citations by year
2026: 9 · 2025: 3
FWCI
3.04
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion)
  • GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion)
  • GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, other-oa)
  • MPG.PuRe (Max Planck Society) (submittedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
Funders
  • Deutsche Forschungsgemeinschaft (SFB860, FOR1193, SFB1565, 469281184, SFB1565 P12, SFB1565 P18, SFB1565 P15)
  • Germany’s Excellence Strategy (2067/1-390 729 940, SFB1565)
  • Federal Ministry of Education and Research
  • Ministry of Science, Research and Arts Baden-Württemberg
  • Max Planck Society
  • European Research Council (ERC-StG 945528 IMAP)
  • European Union’s Horizon 2020
  • Marie Skłodowska-Curie (956148)
  • Smith Family Foundation
  • NIH (DP2GM146254)
  • Alex’s Lemonade Foundation Crazy 8 Initiative
  • International Max Planck Research School for Genome Sciences
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
chemical crosslinking, UV crosslinking, protein-nucleic acid interactions, RNA-binding proteins, DNA-binding proteins, in vivo cross-linking, transcriptional repressor, transcriptional activator, Escherichia coli

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