ChIP and input library preparation for histone modifications (H3K4me1, H3K4me3, H3K27ac) were carried out as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol” in https://www.encodeproject.org/documents/), and ChIP and input library preparation for CTCF were also performed as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol for MicroChIP” in https://www.encodeproject.org/documents/). ChIP-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 or HiSeq2500 protocols (Illumina, San Diego, CA).