Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry

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• dc.contributor.author Reim, Alexander
• dc.contributor.author Ackermann, Roland
• dc.contributor.author Font Mateu, Jofre, 1977-
• dc.contributor.author Kammel, Robert
• dc.contributor.author Beato, Miguel
• dc.contributor.author Nolte, Stefan
• dc.contributor.author Mann, Matthias
• dc.contributor.author Russmann, Christoph
• dc.contributor.author Wierer, Michael, 1982-
• dc.date.accessioned 2020-10-16T06:33:59Z
• dc.date.available 2020-10-16T06:33:59Z
• dc.date.issued 2020
• dc.description.abstract Transcription factors (TFs) regulate target genes by specific interactions with DNA sequences. Detecting and understanding these interactions at the molecular level is of fundamental importance in biological and clinical contexts. Crosslinking mass spectrometry is a powerful tool to assist the structure prediction of protein complexes but has been limited to the study of protein-protein and protein-RNA interactions. Here, we present a femtosecond laser-induced crosslinking mass spectrometry (fliX-MS) workflow, which allows the mapping of protein-DNA contacts at single nucleotide and up to single amino acid resolution. Applied to recombinant histone octamers, NF1, and TBP in complex with DNA, our method is highly specific for the mapping of DNA binding domains. Identified crosslinks are in close agreement with previous biochemical data on DNA binding and mostly fit known complex structures. Applying fliX-MS to cells identifies several bona fide crosslinks on DNA binding domains, paving the way for future large scale ex vivo experiments.
• dc.format.mimetype application/pdf
• dc.identifier.citation Reim A, Ackermann R, Font-Mateu J, Kammel R, Beato M, Nolte S, Mann M, Russmann C, Wierer M. Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry. Nat Commun. 2020; 11(1):3019. DOI: 10.1038/s41467-020-16837-x
• dc.identifier.doi http://dx.doi.org/10.1038/s41467-020-16837-x
• dc.identifier.issn 2041-1723
• dc.identifier.uri http://hdl.handle.net/10230/45496
• dc.language.iso eng
• dc.publisher Nature Research
• dc.relation.ispartof Nat Commun. 2020; 11(1):3019
• dc.rights © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword DNA-binding proteins
• dc.subject.keyword Mass spectrometry
• dc.subject.keyword Proteomics
• dc.subject.keyword Structural biology
• dc.subject.keyword Transcription
• dc.title Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion