For ChIP-seq and ChIP-exo experiments, cells were lysed, and chromatin pellets were isolated and then solubilized and fragmented by sonication. Fragmented chromatin was then subject to immunoprecipitation using antibodies against protein of interest. RNA was extracted using TRIzol reagent (Thermo 15596026). Illumina Ribo-Zero rRNA Removal Kit (MRZH116) was used with DNase-treated total RNA sample to remove ribosomal RNA. ChIP-seq libraries were prepared according to standard Illumina's instructions for HiSeq2000. Briefly, DNA was end-repaired, and ligated to sequencing adaptors, then PCR amplified and gel purified. The purified DNA libraries were sequenced following the manufacturer's protocols. For ChIP-exo libraries, while immunoprecipitates were still on the beads, samples were end-repaired, and ligated to a first sequencing adaptor, and subjected to lambda exonuclease digestion. Samples were then eluted from the beads and converted to double-stranded DNA by primer annealing and extension. A second sequencing adaptor was then ligated to exonuclease treated ends, then DNA was PCR amplified, gel purified, and sequenced. ATAC-seq libraries were prepared as described previously (Buenrostro et al., 2013). Briefly, cells were lysed and spun down. The pellet was resuspended in 50 ul of the transposase reaction mix containing 2.5 μL Tn5 transposase and sequencing adaptors (Illumina DNA Library Preparation Kit, FC-121-1030), and incubated for 30 min at 37 °C. The purified DNA was PCR amplified and sequenced. RNA-seq libraries were prepared for sequencing using standard Illumina protocols. DNase-seq libraries were prepared as described previously (He et al., 2014). Briefly, cells were lysed and spun down. The pellet was resuspended in 500 uL pre-warmed 15 mM Tris buffer A (pH8.0) containing 15 mM NaCl, 60 mM KCl, and 0.5 mM spermidine, and then add different amounts (0, 25, 50, and 75U) of DNase I (Roche, 04716728001) for 5 min at 37C. The reactions were terminated by 500 uL Stop buffer containing 0.5 mM spermidine and 1 ug of RNase, and incubated at 55C for 15 min. The purified DNA was sequenced by following standard Illumina protocols.