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

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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.

In: Nature Communications, Vol. 11, No. 1, 15.06.2020, p. 3019.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Reim, A, Ackermann, R, Font-Mateu, J, Kammel, R, Beato, M, Nolte, S, Mann, M, Russmann, C & Wierer, M 2020, 'Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry', Nature Communications, vol. 11, no. 1, pp. 3019. https://doi.org/10.1038/s41467-020-16837-x

APA

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

Vancouver

Reim A, Ackermann R, Font-Mateu J, Kammel R, Beato M, Nolte S et al. Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry. Nature Communications. 2020 Jun 15;11(1):3019. https://doi.org/10.1038/s41467-020-16837-x

Author

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. In: Nature Communications. 2020 ; Vol. 11, No. 1. pp. 3019.

Bibtex

@article{9d19c127ef61409793bcdea1d3ea79fd,
title = "Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry",
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.",
author = "Alexander Reim and Roland Ackermann and Jofre Font-Mateu and Robert Kammel and Miguel Beato and Stefan Nolte and Matthias Mann and Christoph Russmann and Michael Wierer",
year = "2020",
month = jun,
day = "15",
doi = "10.1038/s41467-020-16837-x",
language = "English",
volume = "11",
pages = "3019",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "nature publishing group",
number = "1",

}

RIS

TY - JOUR

T1 - Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry

AU - Reim, Alexander

AU - Ackermann, Roland

AU - Font-Mateu, Jofre

AU - Kammel, Robert

AU - Beato, Miguel

AU - Nolte, Stefan

AU - Mann, Matthias

AU - Russmann, Christoph

AU - Wierer, Michael

PY - 2020/6/15

Y1 - 2020/6/15

N2 - 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.

AB - 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.

U2 - 10.1038/s41467-020-16837-x

DO - 10.1038/s41467-020-16837-x

M3 - Journal article

C2 - 32541649

VL - 11

SP - 3019

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

ER -

ID: 243474351