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

Reim, A., Ackermann, R., Font-Mateu, J., Kammel, R., Beato, M., Nolte, S., et al. (2020). Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry. Nature Communications, 11(1): 3019. doi:10.1038/s41467-020-16837-x.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0007-18AD-C Version Permalink: http://hdl.handle.net/21.11116/0000-0007-18AE-B
Genre: Journal Article

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 Creators:
Reim, Alexander1, Author              
Ackermann, Roland2, Author
Font-Mateu, Jofre2, Author
Kammel, Robert2, Author
Beato, Miguel2, Author
Nolte, Stefan2, Author
Mann, Matthias1, Author              
Russmann, Christoph2, Author
Wierer, Michael1, Author              
Affiliations:
1Mann, Matthias / Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Max Planck Society, ou_1565159              
2external, ou_persistent22              

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Free keywords: COLLISION-INDUCED DISSOCIATION; PROGESTERONE-RECEPTOR; RECOMBINANT HISTONES; CRYSTAL-STRUCTURE; STRUCTURAL BASIS; BINDING DOMAIN; PROTEIN; REPLICATION; FRAGMENTATION; PEPTIDESScience & Technology - Other Topics;
 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.

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Language(s): eng - English
 Dates: 2020-06
 Publication Status: Published online
 Pages: 14
 Publishing info: -
 Table of Contents: Data availability:
The MS proteomics data have been deposited to the ProteomeXchange Consortium62 (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository63 with the dataset identifier PXD014898. All other data are available from the corresponding authors on reasonable request.
 Rev. Type: Peer
 Degree: -

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Title: Nature Communications
  Abbreviation : Nat. Commun.
Source Genre: Journal
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Publ. Info: London : Nature Publishing Group
Pages: - Volume / Issue: 11 (1) Sequence Number: 3019 Start / End Page: - Identifier: ISSN: 2041-1723
CoNE: https://pure.mpg.de/cone/journals/resource/2041-1723