Total RNA was extracted using standard Trizol protocol. ChIP/CHART/Hi-C-enriched and input DNA were extracted with phenol:chloroform. RNA-seq libraries were prepared by dUTP-mediated directional RNA-seq following NEBNext Ultra directional RNA library preparation protocol. ChIP-seq and Hi-C libraries were prepared by NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina. CHART-seq libraries were generated by NEBNext Ultra DNA Library Prep Kit for Illumina. Paired-end 50 or 69-cycle with Illumina HiSeq