Profiling of PML-body associated regions

The promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various proteins including several chromatin regulators, and physically associates with chromatin. To address functional roles of the PML-chromatin association, we conducted genome-wide profiling of PML body-associated regions. We performed genome-wide profiling of genomic regions associated with PML bodies in mESCs. Cells were treated with H2O2 to trigger labeling of chromatin with biotin (H2O2+). Experimental negative controls (H2O2-), where the H2O2 treatment was omitted, were also analyzed. Sequence reads were trimmed by using Trimmomatic, then mapped to repeat masked mm10 using bowtie2 version 2.3.5.1 with parameter -N1. ENCODE blacklisted regions and grey list prepared by chipseq-greylist were subsequently removed using bedtools. BigWig files were generated by using bamCompare with option --scaleFactorsMethod SES --operation subtract.