Flow-diagram of standardized mono-nucleosomal DNA collection. A standardized amount of whole-cell extract (WCE) is used as input for MNase digestions to isolate nucleosomal DNA and collect mono-nucleosomal fragments. A small fraction of nucleosomal DNA then is separated following MNase digestion using gel electrophoresis. The extent of MNase digestion is compared between these samples by calculating a Pearson correlation (r) for relative front (i.e. separation relative to standard fragment sizes) for the migrating chromatin DNA populations in each lane. ‘Matched’ digests are selected as two complete-digested (100% Monos) samples that have a correlation coefficient r > 0.9 (yellow highlight). Remaining nucleosomal DNA (not loaded onto the gel) is then column purified and used in downstream analysis, thus bypassing the need for gel-excision.
Rizzo et al. BMC Molecular Biology 2012 13:15 doi:10.1186/1471-2199-13-15