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

Alexander Reim, Roland Ackermann, Jofre Font-Mateu, Robert Kammel, Miguel Beato, Stefan Nolte, Matthias Mann, Christoph Russmann () and Michael Wierer ()
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Alexander Reim: Max-Planck Institute of Biochemistry
Roland Ackermann: Friedrich-Schiller-Universität Jena
Jofre Font-Mateu: The Barcelona Institute of Science and Technology
Robert Kammel: Friedrich-Schiller-Universität Jena
Miguel Beato: The Barcelona Institute of Science and Technology
Stefan Nolte: Friedrich-Schiller-Universität Jena
Matthias Mann: Max-Planck Institute of Biochemistry
Christoph Russmann: University of Applied Sciences and Arts Hildesheim/Holzminden/Goettingen (HAWK)
Michael Wierer: Max-Planck Institute of Biochemistry

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-16837-x

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