Trendel Jakob, Trendel Simon, Sha Shuyao, Greulich Franziska, Goll Sandra, Wudy Susanne I, Kleigrewe Karin, Kubicek Stefan, Uhlenhaut N Henriette, Kuster Bernhard
Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich (TUM), Freising, Germany.
Munich, Bavaria, Germany.
Cell. 2025 Aug 7;188(16):4424-4440.e17. doi: 10.1016/j.cell.2025.04.037. Epub 2025 May 22.
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.
在人类细胞中，DNA与组蛋白、RNA以及染色质相关蛋白结合在一起，形成一种粘性凝胶。在任何给定时刻，只有蛋白质组的一个子集能够实际接触到DNA并组织其结构、转录、复制、修复以及其他重要的分子功能。我们开发了一种“零距离”光交联方法来量化活细胞中与DNA直接接触的蛋白质。通过收集人类乳腺癌细胞的DNA相互作用组，我们展示了一个包含一千多种能够实际接触DNA的蛋白质图谱，以及数百个肽-核苷酸交联，这些交联以单氨基酸分辨率精确确定了蛋白质-DNA界面。对来自不同处理细胞的DNA相互作用组进行定量比较，再现了关键转录因子以及DNA修复蛋白的招募情况，并揭示了在几分钟时间尺度上染色质可及性的快速作用限制因子。这为以无假设方式探索基因组调控开辟了一条直接途径，适用于许多生物体和系统。
