I've read that an alternative to sonication is fragmentation by MNase. But people seem to have different opinions on the benefits or inconveniences of using one or the other.
Can some one give me a good reason for using one over the other?
Alternatively, why not using a cocktail of restriction enzymes to to the fragmentation?
Hi,
Sonication is the most random way to get fragmented chromatin. Moreover, enzymatic digestion on fixed cells is not efficient ( DNA sequence is hidden by fixed proteins) and biased (open chromatin is more sensitive to digestion comparing to inactive one). MNase is mainly used for native ChIP and require some additional optimization. Restriction enzymes will be even less random and probably the same problem of inaccessibility of DNA sequence.
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