You could use density gradient centrifugation on MNase digested samples, with MNase concentration which gives moderate digestion, such that most fragments are present in digest. Running the centrigual fractions on agarose gel in control and treated cells should give you a difference in level of global compaction. You can also do a comet assay for DNA damage analysis on single cells using microscopy. Atomic force microscopy is another technique to use.
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