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A transient ischemic environment induces reversible compaction of chromatin

By Ina Kirmes, Aleksander Szczurek, Kirti Prakash, Iryna Charapitsa, Christina Heiser, Michael Musheev, Florian Schock, Karolina Fornalczyk, Dongyu Ma, Udo Birk, Christoph Cremer, George Reid

Posted 21 Aug 2015
bioRxiv DOI: 10.1101/025221 (published DOI: 10.1186/s13059-015-0802-2)

The environmental effects of ischemia on chromatin nanostructure were evaluated using single molecule localisation microscopy (SMLM) of DNA binding dyes. 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 of the order of 40 to 700 nm in dimension. OND induced chromatin compaction is reversible, and upon restitution of normoxia and nutrients, chromatin transiently adopts a significantly more open structure than in untreated cells. We show that this compacted state of chromatin reduces transcription, while the open chromatin structure following recovery has a higher transcriptional rate than in untreated cells. Digestion of chromatin with DNAseI and DNA binding dye loading assays confirm that OND induces compaction of chromatin and a general redistribution of chromatin to the nuclear periphery. Mechanistically, chromatin compaction is associated with a depletion of intracellular ATP and a redistribution of the cellular polyamine pool into the nucleus. Additionally, Fluorescence Recovery After Photobleaching (FRAP) shows that core histones are not displaced from compacted chromatin and that 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. 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.

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