DOI: 10.5061/dryad.d3j00
title: Data from: A transient ischemic environment induces reversible compaction of chromatin

description: 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.
description: Part 1 of 11 Zip file of
 primary data for "A transient ischaemic environment induces
 reversible compaction of chromatin"All image sets for the
 Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work
 (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts;
 240min:9 expts). All image sets for the YOYO-1 and EdU Single Molecule
 Localization Microscopy work. All image sets for the DNAseI experiments
 (UT:11 expts; OND:11 expts). All image sets for the H2B-mCherry FRAP
 study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study
 (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts). The
 datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at
 con, 0, 2, 5, 15 30 mins, 1 and 4 hours.GenomeBiology_submission.zip.001Part 2 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts). All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work. All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts). All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts). The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.GenomeBiology_submission.zip.002Part 3 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts). All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work. All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts). All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts). The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.GenomeBiology_submission.zip.003Part 4 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts). All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work. All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts). All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts). The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.GenomeBiology_submission.zip.004Part 5 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts). All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work. All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts). All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts). The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.GenomeBiology_submission.zip.005Part 6 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts). All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work. All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts). All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts). The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.GenomeBiology_submission.zip.006Part 7 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts). All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work. All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts). All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts). The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.GenomeBiology_submission.zip.007Part 8 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts). All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work. All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts). All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts). The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.GenomeBiology_submission.zip.008Part 9 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts). All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work. All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts). All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts). The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.GenomeBiology_submission.zip.009Part 10 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts). All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work. All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts). All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts). The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.GenomeBiology_submission.zip.010Part 11 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts). All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work. All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts). All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts). The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.GenomeBiology_submission.zip.011