An assay for testing general chromatin compaction??? - (Oct/18/2012 )
I would like to test if the global level of chromatin compaction in the cells of interest changes after a treatment. I know that you can use MNase for a specific genomic location, but what if you'd like to see if there is any global effect? Is it possible to couple MNase with WB or any other method to get the answer to this? Or are the only alternatives sequencing-based methods (eg MNase-seq, FAIRE-seq)?
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.