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.
I: Nature Communications, Bind 11, Nr. 1, 15.06.2020, s. 3019.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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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