A transient ischemic environment induces reversible compaction of chromatin

Abstract

Background: Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy 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 of the cardiomyocyte cell line HL-1 induces a previously undescribed chromatin architecture, consisting of large, chromatin-sparse voids interspersed between DNA-dense hollow helicoid structures 40-700 nm in dimension. The 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 oxygen and nutrient deprivation induces compaction of chromatin. 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, 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 ischemia has on the nuclear architecture of cells.

The three‐dimensional cancer nucleus

“…(Figure 6B).Although no additional cancers have yet been investigated, one may speculate that such changes probably affect other cancers well.Another line of evidence demonstrated changes in nuclear DNA organization as a result of ischemic stress34 (Figure 6C): DNA-poor spaces increased significantly after ischemia. What is more, when ischemia subsided, the nuclear organization resumed its regular order.…”

A guide to visualizing the spatial epigenome with super‐resolution microscopy

“…The chemical modifications (e.g., acetylation, methylation) on histone tails regulate the compaction of nucleosomes into higher-order chromatin structure and reflect its functional state marked by each histone modification. Therefore, higher-order chromatin structure is often visualized via fluorescence microscopic imaging of three fluorescently labeled targets -DNA [83][84][85][86], core histone proteins [23,[87][88][89] and histone modifications [90][91][92] (summarized in Fig. 2).…”

Super‐resolution structure of DNA significantly differs in buccal cells of controls and Alzheimer's patients

“…There may be dynamic changes in the organization of the genome structure and its associated function that enable the remodeling of the (Kirmes et al, 2015; for review, see Cremer et al, 2015).…”