Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.
Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
Mol Syst Biol. 2021 Jun;17(6):e9760. doi: 10.15252/msb.20209760.
Spatial organization and gene expression of mammalian chromosomes are maintained and regulated in conjunction with cell cycle progression. This is perturbed once cells enter senescence and the highly abundant HMGB1 protein is depleted from nuclei to act as an extracellular proinflammatory stimulus. Despite its physiological importance, we know little about the positioning of HMGB1 on chromatin and its nuclear roles. To address this, we mapped HMGB1 binding genome-wide in two primary cell lines. We integrated ChIP-seq and Hi-C with graph theory to uncover clustering of HMGB1-marked topological domains that harbor genes involved in paracrine senescence. Using simplified Cross-Linking and Immuno-Precipitation and functional tests, we show that HMGB1 is also a bona fide RNA-binding protein (RBP) binding hundreds of mRNAs. It presents an interactome rich in RBPs implicated in senescence regulation. The mRNAs of many of these RBPs are directly bound by HMGB1 and regulate availability of SASP-relevant transcripts. Our findings reveal a broader than hitherto assumed role for HMGB1 in coordinating chromatin folding and RNA homeostasis as part of a regulatory loop controlling cell-autonomous and paracrine senescence.
哺乳动物染色体的空间组织和基因表达与细胞周期进程的结合而得到维持和调控。一旦细胞进入衰老状态，高丰度的 HMGB1 蛋白从核内耗尽，作为细胞外促炎刺激物发挥作用，这种调控就会受到干扰。尽管 HMGB1 具有重要的生理意义，但我们对其在染色质上的定位及其核内作用知之甚少。为了解决这个问题，我们在两种原代细胞系中进行了全基因组范围内的 HMGB1 结合图谱绘制。我们将 ChIP-seq 和 Hi-C 与图论相结合，揭示了 HMGB1 标记的拓扑结构域的聚类，这些结构域含有参与旁分泌衰老的基因。使用简化的交联和免疫沉淀以及功能测试，我们表明 HMGB1 也是一种真正的 RNA 结合蛋白（RBP），能结合数百种 mRNA。它呈现出一个富含与衰老调控相关的 RBPs 的相互作用组。这些 RBPs 的许多 mRNAs 直接被 HMGB1 结合，并调节与 SASP 相关的转录本的可用性。我们的研究结果揭示了 HMGB1 在协调染色质折叠和 RNA 动态平衡方面的作用比以前认为的更为广泛，它是一个控制细胞自主和旁分泌衰老的调节环的一部分。
