ChIP-seq: Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For native ChIP-seq, cells were collected and digested by MNase to get the mono-nucleosome. For BrdU-IP-seq, genomic ChIP-seq: DNA were extracted from cells and then sonicated to 200-500bp. Libraries were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq. NS-seq: The genomic DNA was extracted by DNAzol. Then the DNA was denatured by boiling 10 mins at 100 °C and loaded onto 30ml neutral 5%-30% sucrose gradients. The mixture was centrifuged in SW28 rotor at 25000rpm for 20 hours. 1 ml-fraction was withdrawn from the top of the gradients. DNA fragments ranged from 0.5-2.5Kb were collected and purified. Half of the total purified DNA was treated with RNAase A. NS-seq: The single strand DNA was converted to double strand DNA by BioPrime Array CGH Genomic Labeling System (life technology). DNA library for Immunila was prepared using a NEBNext Ultra DNA Library Prep Kit (NEB) according to the manufactory's instruction. RNA-seq: RNA was extracted using Trizol (Invitrogen) according to the manufacturer's instruction. RNA-seq: For RNA-seq, libraries were prepared according to the Illumina TruSeq protocol.