HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence [ChIP-seq]

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 harbour genes required for paracrine senescence. Using sCLIP 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 the availability of SASP-relevant transcripts. Our findings highlight 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构象与基因表达，会伴随细胞周期进程得到维持与调控。当细胞进入衰老状态后，该调控稳态会被打破：细胞核内高丰度的HMGB1蛋白会被耗竭，并转而作为细胞外促炎刺激因子发挥作用。尽管HMGB1具有重要的生理学意义，但目前学界对其在染色质上的定位以及核内功能仍知之甚少。为解决这一科学问题，我们在两种原代细胞系中完成了HMGB1全基因组结合位点的定位分析。我们整合染色质免疫共沉淀测序（ChIP-seq）、高通量染色体构象捕获（Hi-C）与图论分析方法，揭示了HMGB1标记的拓扑结构域的聚集现象，这类结构域携带着调控旁分泌衰老所需的功能基因。通过sCLIP与功能实验，我们证实HMGB1同时也是一种确凿的RNA结合蛋白（RBP），可与数百种mRNA相结合。其相互作用组富含与衰老调控相关的RBP，其中多数RBP的mRNA会被HMGB1直接结合，并调控与衰老相关分泌表型（senescence-associated secretory phenotype, SASP）相关的转录本的可及性。本研究结果表明，HMGB1在协调染色质折叠与RNA稳态中的作用范围较此前预想更为广泛，其作为调控环路的核心组分，同时参与调控细胞自主性衰老与旁分泌衰老过程。