Nuclei were treated with MPE-Fe(II). The reaction was quenched by addition of bathophenanthroline to ~6 mM and the soluble fraction was extracted. The sample was immunoprecipitated with an antibody against histone H3 (Abcam ab1791). After elution, the sample was treated with RNase A to remove RNA. Then the sample was treated wtih proteinase K and was extracted with phenol and chloroform to remove proteins. The DNA was isolated by precipitation with ethanol. DNA was end-repaired using End-It DNA End-Repair Kit (Epicenter) and 3' ends were adenylated by treating the samples with Klenow (exo-) (NEB) in the presence of dATP. The samples were then ligated to Illumina TruSeq adapters. The ligated products were run on agarose gel and were purified using Qiagen MinElute columns. The ligated products were then PCR-amplified using KAPA master mix. The amplified products were run on agarose gel and were purified using Qiagen MinElute columns.