In CHIP-seq, cells are fixed, washed, and lysed to purify the nuceli. Then chromatin were fragmented with Covaris, and mixed with antibody and beads to pull down the bound fraction as described in the manuscript. In TMP-seq, protein and RNA are first crosslinked in TMP solution with UV; then genomic DNA are purified and sheared with Covaris. In ATAC_seq, the 50,000 cells are washed and tagmented by Tn5 for 30min. Standard CHIP-seq libraries made using NEBnext Ultra II kit from chipped DNA. TMP_seq and ATAC-seq libraries were constructed following published protocols. CHIP-seq and TMP_seq were sequencing in Illuma in Single end. ATAC_seq were sequenced in Paired end.