Single-nucleosome imaging reveals principles of transient multiscale chromatin unfolding triggered by histone ADP-ribosylation at DNA lesions

Timely access to DNA lesions is crucial for genome integrity. This process requires profound remodeling of densely packed chromatin to establish a repair-competent architecture. However, limited resolution has made it impossible to fully understand these remodeling events. Here, combining microirradiation with live-cell multiscale imaging, we report that DNA damage-induced changes in genome packing rely on the conformational behaviour of the chromatin fiber. Immediately after damage, a transient increase in nucleosome mobility switches chromatin from a densely-packed state to a looser conformation, making it accessible to repair. While histone poly-ADP-ribosylation is required to trigger this switch, mono-ADP-ribosylation is sufficient to maintain the open-chromatin state. The removal of these histone marks by the ARH3 hydrolase then leads to chromatin recondensation. Together, our multiscale study of chromatin dynamics establishes a global model: distinct waves of histone ADP-ribosylation control nucleosome mobility, triggering a transient breathing of chromatin, crucial for initiating the DNA damage response.

及时实现DNA损伤（DNA lesions）的可及性，对于维持基因组完整性至关重要。这一过程需要对高度致密的染色质（chromatin）进行深度重塑，以构建具备修复能力的染色质结构。然而，受限于成像分辨率，此前无法完全阐明这类重塑事件的具体机制。本研究将显微辐照（microirradiation）与活细胞多尺度成像（live-cell multiscale imaging）相结合，揭示了DNA损伤诱导的基因组包装变化依赖于染色质纤维的构象动态行为。损伤发生后即刻，核小体（nucleosome）流动性的瞬时升高会将染色质从致密状态转变为松散构象，从而使其能够被修复因子所接触。尽管组蛋白（histone）多聚ADP核糖基化（poly-ADP-ribosylation）是触发这一构象转变的必要条件，但单ADP核糖基化（mono-ADP-ribosylation）足以维持染色质的开放状态。随后，ARH3水解酶（ARH3 hydrolase）会清除这些组蛋白修饰，进而促使染色质重新致密化。综上，我们这项针对染色质动态的多尺度研究构建了一个普适性模型：组蛋白ADP核糖基化的不同时相波峰调控核小体流动性，进而触发染色质的瞬时呼吸动态，这对于启动DNA损伤应答（DNA damage response）至关重要。