Native Chromatin immunoprecipitation (N-ChIP) assay was performed as previously described. Approximately 10 million of ESC s were used for each ChIP and massive parallel sequencing (ChIP-Seq) experiment. In brief, chromatin pellets were briefly digested with MNase (New England BioLabs) and the mononucleosomes were monitored by electrophoresis.5ug anti-H2A.X antibodies (active motif 39689)were used per ChIP experiment. Libraries were prepared according to Illumina's standard protocol, with instructions accompanying the DNA Sample Kit