2. Academic Validation
  3. The human proteome with direct physical access to DNA

The human proteome with direct physical access to DNA

  • Cell. 2025 Aug 7;188(16):4424-4440.e17. doi: 10.1016/j.cell.2025.04.037.
Jakob Trendel 1,  Simon Trendel 2,  Shuyao Sha 1,  Franziska Greulich 3,  Sandra Goll 4,  Susanne I Wudy 5,  Karin Kleigrewe 5,  Stefan Kubicek 4,  N Henriette Uhlenhaut 6,  Bernhard Kuster 7
Affiliations

Affiliations

  • 1 Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich (TUM), Freising, Germany.
  • 2 Munich, Bavaria, Germany.
  • 3 Metabolic Programming, TUM School of Life Sciences, ZIEL-Institute for Food & Health, Technical University of Munich (TUM), Freising, Germany.
  • 4 CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
  • 5 Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich (TUM), Freising, Germany.
  • 6 Metabolic Programming, TUM School of Life Sciences, ZIEL-Institute for Food & Health, Technical University of Munich (TUM), Freising, Germany; Institute for Diabetes and Obesity (IDO) & Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), Neuherberg, Germany.
  • 7 Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich (TUM), Freising, Germany. Electronic address: kuster@tum.de.
PMID: 40409270 DOI: 10.1016/j.cell.2025.04.037
Abstract

In a human cell, DNA is packed with histones, RNA, and chromatin-associated proteins, forming a cohesive gel. At any given moment, only a subset of the proteome has physical access to the DNA and organizes its structure, transcription, replication, repair, and Other essential molecular functions. We have developed a "zero-distance" photo-crosslinking approach to quantify proteins in direct contact with DNA in living cells. Collecting DNA interactomes from human breast Cancer cells, we present an atlas of over one thousand proteins with physical access to DNA and hundreds of peptide-nucleotide crosslinks pinpointing protein-DNA interfaces with single-amino-acid resolution. Quantitative comparisons of DNA interactomes from differentially treated cells recapitulate the recruitment of key transcription factors as well as DNA repair proteins and uncover fast-acting restrictors of chromatin accessibility on a timescale of minutes. This opens a direct way to explore genomic regulation in a hypothesis-free manner, applicable to many organisms and systems.

Keywords

DNA-binding domains; DNA-binding proteins; DNA-interacting proteome; IDRs; chromatin proteomics; intrinsically disordered regions; mass spectrometry; nucleotide-peptide hybrids; photo-crosslinking; physical protein-DNA interactions; transcription factors.

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