Data from: A transient ischemic environment induces reversible compaction of chromatin

Background: Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischaemia on chromatin nanostructure were investigated using single molecule localisation microscopy (SMLM) of DNA binding dyes and of acetylated histones, by the sensitivity of chromatin to digestion with DNAseI, and by Fluorescence Recovery After Photobleaching (FRAP) of core and linker histones. Results: Short-term oxygen and nutrient deprivation (OND) of the cardiomyocyte cell-line HL-1induces a previously undescribed chromatin architecture, consisting of large, chromatin sparse voids interspersed between DNA-dense hollow helicoid structures 40 to 700 nm in dimension. OND induced chromatin compaction is reversible, and upon restitution of normoxia and nutrients, chromatin transiently adopts a more open structure than in untreated cells. The compacted state of chromatin reduces transcription, while the open chromatin structure induced upon recovery provokes a transitory increase in transcription. Digestion of chromatin with DNAseI confirms that OND induces compaction of chromatin. Mechanistically, chromatin compaction is associated with depletion of ATP and redistribution of the polyamine pool into the nucleus. FRAP demonstrates that core histones are not displaced from compacted chromatin; however, the mobility of linker histone H1 is considerably reduced by OND treatment, to an extent that far exceeds the difference in histone H1 mobility between heterochromatin and euchromatin. Conclusions: These studies exemplify the dynamic capacity of chromatin architecture to physically respond to environmental conditions, directly link cellular energy status to chromatin compaction and provide insight into the effect ischaemia has on the nuclear architecture of cells.

背景：细胞可通过即时的转录、翻译及代谢反应感知并适应缺氧与营养匮乏应激。本研究通过DNA结合染料与乙酰化组蛋白的单分子定位显微镜（single molecule localisation microscopy, SMLM）成像、染色质对脱氧核糖核酸酶I（DNAseI）消化的敏感性检测，以及核心组蛋白与连接组蛋白的荧光漂白后恢复（Fluorescence Recovery After Photobleaching, FRAP）实验，探究了缺血对染色质纳米结构的影响。结果：针对心肌细胞系HL-1的短期氧与营养剥夺（Short-term oxygen and nutrient deprivation, OND）可诱导出一种此前未见报道的染色质结构：大量染色质稀疏的空隙散布于尺寸为40~700 nm的DNA密集型中空螺旋状结构之间。OND诱导的染色质浓缩具有可逆性，在恢复常氧与营养供给后，染色质会暂时呈现比未处理细胞更为开放的结构。染色质的浓缩状态会降低转录活性，而恢复阶段诱导的开放染色质结构则会引发转录水平的短暂升高。脱氧核糖核酸酶I消化染色质实验证实，OND可诱导染色质浓缩。从机制层面而言，染色质浓缩与ATP耗竭及多胺池重新分布进入细胞核密切相关。FRAP实验结果显示，核心组蛋白并未从浓缩的染色质上解离；但经OND处理后，连接组蛋白H1的流动性显著降低，其降低幅度远高于异染色质与常染色质间组蛋白H1流动性的差异。结论：本研究证实了染色质结构具备通过物理方式响应环境变化的动态能力，直接将细胞能量状态与染色质浓缩建立关联，并为缺血对细胞细胞核结构的影响提供了新的认知视角。