PXD014898 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Mapping protein-DNA interactions by UV femtosecond laser crosslinking and mass spectrometry analysis |
Description | Transcription factors (TFs) regulate target genes by specific interaction with DNA sequences. Detecting and understanding these interactions on molecular level is of fundamental interest in both biological and clinical context. Crosslinking mass spectrometry is a powerful tool to assist structure prediction of protein complexes by providing direct evidence for physical contacts on sub-molecular level. Yet, until now it has been limited to the study of protein-protein and protein-RNA interactions. Here, we developed a femtosecond laser induced crosslinking mass spectrometry (fLiX-MS) workflow, which allows mapping of protein-DNA contacts at single nucleotide and up to single amino acid resolution. Applying the method to in-vitro assembled nucleosomes and recombinant TF-DNA complexes, our method proved both versatile and highly specific for mapping DNA binding domains. While for Nuclear factor 1 (NF1) the detected crosslinks were in perfect agreement with previous biochemical data on DNA binding, crosslinks for the TATA box binding protein (TBP) fitted to the known crystal structure. We further identified several protein-DNA interactions for the nucleosome and TBP, which were rather distant in the crystal-structure, indicating, that our method is capable to detect structural flexibility reflected in distinct conformational states. Moreover, applying the fLiX-MS workflow to cells, we detected several bona-fide crosslinks on DNA-binding domains, proving the applicability of the method for future large scale in-vivo experiments. |
HostingRepository | PRIDE |
AnnounceDate | 2020-06-22 |
AnnouncementXML | Submission_2020-06-21_22:30:08.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Michael Wierer |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | carbamoylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2019-08-02 07:53:23 | ID requested | |
⏵ 1 | 2020-06-21 22:30:09 | announced | |
Publication List
Reim A, Ackermann R, Font-Mateu J, Kammel R, Beato M, Nolte S, Mann M, Russmann C, Wierer M, Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry. Nat Commun, 11(1):3019(2020) [pubmed] |
Keyword List
curator keyword: Technical |
submitter keyword: Mass spectrometry, transcription factor, femtosecond laser, protein-DNA crosslinking, UV |
Contact List
Michael Wierer |
contact affiliation | Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Am Klopferspitz 18 D-82152 Martinsried Germany |
contact email | wierer@biochem.mpg.de |
lab head | |
Michael Wierer |
contact affiliation | Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany |
contact email | wierer@biochem.mpg.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD014898
- Label: PRIDE project
- Name: Mapping protein-DNA interactions by UV femtosecond laser crosslinking and mass spectrometry analysis