Promoter Capture HiC-Seq: we used the same protocol at Montefiori et al., (Elife, 2018 Jul 10; 7) BS-seq: Genomic DNA was isolated from 3×106 cells using Qiagen DNeasy blood and tissue kit (Cat #: 69506). The bisulfite conversion was performed using the EZ DNA Methylation-Gold™ Kit (Cat #: D5005) from Zymo Research. Whole-genome bisulfite sequencing libraries were prepared from 50 ng converted DNA using Illumina TruSeq® DNA Methylation Kit (Cat #: EGMK91324), which was performed following the manufacturer's protocol. Promoter Capture HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 3000 (Illumina). BS-seq: standard RNA-Seq library preparation was performed following the genomic DNA protocol with 20% PhiX. 50 cycles of sequencing data were acquired on HiSeq 3000 (Illumina)