I haven't seen this problem reported before, and was wondering if anyone had any thoughts or solutions.
We are sonicating formaldehyde cross-linked DNA for ChIP using a Misonix S-4000 sonicator. After running the fragments on a gel, we see a smear up to about 3 kb, and bright band of fragments around 100-200 bp (about mononucleosomal length). If we continue to sonicate, eventually the smear will disappear, but all fragments will be 100-200 bp. We never see the enrichment of fragments from ~200-500 bp that we are aiming for. The fragments are always too small.
We've tried cross-linking from 2-30 minutes, using 0.5-2% formaldehyde, different cell densities, a range of amplitudes and times for sonication. We de-crosslink at 65C overnight, and treat with proteinase K and RNAse A. The samples are from asynchronously growing Hek-293 cells.
Has anyone else seen this, or have any experience with getting too much enrichment on short fragments?