Key Laboratory of Hebei Province for Molecular Biophysics, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300130, China.
School of Exercise and Health, Shanghai University of Sport, Shanghai, 200438, China.
Commun Biol. 2024 Sep 30;7(1):1216. doi: 10.1038/s42003-024-06904-0.
Formaldehyde (FA) is a chemical that facilitates crosslinking between DNA and proteins. It is widely used in various biochemical assays, such as chromosome conformation capture (3C) and Chromatin Immunoprecipitation (ChIP). While the concentration and temperature of FA treatment are recognized as crucial factors in crosslinking, their quantitative effects have largely remained unexplored. In this study, we employed 3C as a model system to systematically assess the impacts of these two factors on crosslinking. Our findings indicate that the strength of crosslinking significantly influences chromatin conformation detection at nearly all known structural levels. Specifically, a delicate balance between sensitivity and reliability is required when detecting higher-level structures, such as chromosome compartments. Conversely, intense crosslinking is preferred when targeting lower-level structures, such as topologically associated domains (TADs) or chromatin loops. Based on our data, we propose a conceptual molecular thermal motion model to elucidate the roles of these two factors in restricting FA crosslinking. Our results not only shed light on the previously overlooked confounding factor in FA crosslinking but also highlight the need for caution in new technology developments that rely on FA crosslinking.
甲醛（FA）是一种促进 DNA 和蛋白质之间交联的化学物质。它广泛用于各种生化测定，如染色体构象捕获（3C）和染色质免疫沉淀（ChIP）。虽然 FA 处理的浓度和温度被认为是交联的关键因素，但它们的定量影响在很大程度上仍未得到探索。在这项研究中，我们采用 3C 作为模型系统，系统地评估了这两个因素对交联的影响。我们的研究结果表明，交联的强度显著影响几乎所有已知结构水平的染色质构象检测。具体来说，在检测更高层次的结构，如染色体区室时，需要在灵敏度和可靠性之间取得微妙的平衡。相反，在靶向较低层次的结构，如拓扑关联域（TAD）或染色质环时，强烈的交联是首选。基于我们的数据，我们提出了一个概念性的分子热运动模型来阐明这两个因素在限制 FA 交联中的作用。我们的结果不仅揭示了 FA 交联中以前被忽视的混杂因素，而且强调了在依赖 FA 交联的新技术发展中需要谨慎。
