Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
Nature. 2024 Apr;628(8007):408-415. doi: 10.1038/s41586-024-07172-y. Epub 2024 Mar 13.
During development, inflammation or tissue injury, macrophages may successively engulf and process multiple apoptotic corpses via efferocytosis to achieve tissue homeostasis. How macrophages may rapidly adapt their transcription to achieve continuous corpse uptake is incompletely understood. Transcriptional pause/release is an evolutionarily conserved mechanism, in which RNA polymerase (Pol) II initiates transcription for 20-60 nucleotides, is paused for minutes to hours and is then released to make full-length mRNA. Here we show that macrophages, within minutes of corpse encounter, use transcriptional pause/release to unleash a rapid transcriptional response. For human and mouse macrophages, the Pol II pause/release was required for continuous efferocytosis in vitro and in vivo. Interestingly, blocking Pol II pause/release did not impede Fc receptor-mediated phagocytosis, yeast uptake or bacterial phagocytosis. Integration of data from three genomic approaches-precision nuclear run-on sequencing, RNA sequencing, and assay for transposase-accessible chromatin using sequencing (ATAC-seq)-on efferocytic macrophages at different time points revealed that Pol II pause/release controls expression of select transcription factors and downstream target genes. Mechanistic studies on transcription factor EGR3, prominently regulated by pause/release, uncovered EGR3-related reprogramming of other macrophage genes involved in cytoskeleton and corpse processing. Using lysosomal probes and a new genetic fluorescent reporter, we identify a role for pause/release in phagosome acidification during efferocytosis. Furthermore, microglia from egr3-deficient zebrafish embryos displayed reduced phagocytosis of apoptotic neurons and fewer maturing phagosomes, supporting defective corpse processing. Collectively, these data indicate that macrophages use Pol II pause/release as a mechanism to rapidly alter their transcriptional programs for efficient processing of the ingested apoptotic corpses and for successive efferocytosis.
在发育、炎症或组织损伤过程中，巨噬细胞可能通过噬作用连续吞噬和处理多个凋亡细胞尸体，以实现组织稳态。巨噬细胞如何快速适应其转录以实现连续的细胞尸体摄取，目前还不完全清楚。转录暂停/释放是一种进化上保守的机制，在此过程中，RNA 聚合酶（Pol）II 启动转录 20-60 个核苷酸，暂停几分钟到几小时，然后释放以产生全长 mRNA。在这里，我们发现巨噬细胞在遇到细胞尸体后的几分钟内，利用转录暂停/释放来引发快速的转录反应。对于人和鼠巨噬细胞，Pol II 暂停/释放对于体外和体内的连续噬作用是必需的。有趣的是，阻断 Pol II 暂停/释放并不妨碍 Fc 受体介导的吞噬作用、酵母摄取或细菌吞噬作用。在不同时间点对噬作用巨噬细胞进行三种基因组方法（精确核运行测序、RNA 测序和转座酶可及染色质测序（ATAC-seq））的数据整合表明，Pol II 暂停/释放控制了特定转录因子和下游靶基因的表达。对转录因子 EGR3 的机制研究，其主要受到暂停/释放的调控，揭示了 EGR3 相关的其他巨噬细胞基因的重编程，这些基因参与细胞骨架和细胞尸体处理。使用溶酶体探针和一种新的遗传荧光报告基因，我们确定了在噬作用期间，暂停/释放在吞噬体酸化中的作用。此外，来自 egr3 缺陷斑马鱼胚胎的小神经胶质细胞显示出对凋亡神经元的吞噬作用减少，并且成熟的吞噬体更少，这支持了细胞尸体处理的缺陷。总之，这些数据表明，巨噬细胞利用 Pol II 暂停/释放作为一种机制，快速改变其转录程序，以有效处理摄入的凋亡细胞尸体，并进行连续的噬作用。
