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Enzymatic vs. acoustic shearing of DNA for ChIP

August 15, 2011

So the question is what is better.  I think it depends on the epitope.  In each image below the two top tracks (V1 tracks) are from acoustic shearing using a tip sonicator and the bottom (V3 tracks) are from enzymatic shearing using micorcoccal nuclease.  As you can see there is a binding site that is only seen with acoustic shearing (top image) and a biding site that is only seen with enzymatic shearing (bottom image).

You can imagine that enzymatic shearing is gentler on epitopes, while acoustic shearing could shear the epitope from the chromatin.  Thus, epitopes that are not directly bound to the DNA may be better suited for enzymatic shearing protocols.  However, for some epitopes it is clear that enzymatic shearing does not produce good data.  The peak seen in the bottom image is from an abundant nucleosomal epitope.  Perhaps, with enzymatic shearing, while the chromatin has been cut down to the mono- and di-nucleosomal level, it is still cross-linked into higher order structures and these higher-order structures produce a lot of background in this situation.

Bottom line, try both methods and see what works better.

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