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Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry
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 struc...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295792/ https://www.ncbi.nlm.nih.gov/pubmed/32541649 http://dx.doi.org/10.1038/s41467-020-16837-x |
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author | Reim, Alexander Ackermann, Roland Font-Mateu, Jofre Kammel, Robert Beato, Miguel Nolte, Stefan Mann, Matthias Russmann, Christoph Wierer, Michael |
author_facet | Reim, Alexander Ackermann, Roland Font-Mateu, Jofre Kammel, Robert Beato, Miguel Nolte, Stefan Mann, Matthias Russmann, Christoph Wierer, Michael |
author_sort | Reim, Alexander |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7295792 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-72957922020-06-19 Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry Reim, Alexander Ackermann, Roland Font-Mateu, Jofre Kammel, Robert Beato, Miguel Nolte, Stefan Mann, Matthias Russmann, Christoph Wierer, Michael Nat Commun Article 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. Nature Publishing Group UK 2020-06-15 /pmc/articles/PMC7295792/ /pubmed/32541649 http://dx.doi.org/10.1038/s41467-020-16837-x Text en © 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/. |
spellingShingle | Article Reim, Alexander Ackermann, Roland Font-Mateu, Jofre Kammel, Robert Beato, Miguel Nolte, Stefan Mann, Matthias Russmann, Christoph Wierer, Michael Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry |
title | Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry |
title_full | Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry |
title_fullStr | Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry |
title_full_unstemmed | Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry |
title_short | Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry |
title_sort | atomic-resolution mapping of transcription factor-dna interactions by femtosecond laser crosslinking and mass spectrometry |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295792/ https://www.ncbi.nlm.nih.gov/pubmed/32541649 http://dx.doi.org/10.1038/s41467-020-16837-x |
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