Fig. 1

Addition of 5-mdCTP in UniNicE-seq workflow. a Schematic diagram showing Nt.CviPII is blocked by 5-methylcytosine in recognition (CCD) sequence. During nick translation, 5-mdCTP can be incorporated at one or both cytosine positions. Nucleotide mixtures containing biotinylated dCTP and 5-mdCTP would allow both labels at CCD sites. Lower panel shows the blocking of nicking by the presence of 5mC at CCD sites. After the nicking reaction, the denatured oligonucleotides were resolved in a urea-acrylamide denaturing gel by electrophoresis. C is control input oligos, − or + indicate the absence or presence of Nt.CviPII in the reaction. mC and btC represent the 5-methylcytosine and biotinylated-cytosine, respectively. Nicked oligonucleotide migrates faster on the denaturing urea gel. b Schematic diagram of the UniNicE-seq method for accessible chromatin library preparation. c Substitution of dATP by Texas Red-conjugated dATP will allow accessible chromatin visualization in the nucleus. d IGV screenshot of the normalized read density of UniNicE-seq using 2.5 U (top track), 25 U (middle track), and 50 U (bottom track) of Nt.CviPII in HCT116 e Venn diagram showing the overlap of peaks in various amounts of Nt.CviPII in the universal NicE-seq (UniNicE-seq) reaction in HCT116 cells.