Genome-wide ChIP-seq Analysis of Transcription Factors and Histone Modifications

ChIP-seq was done as previously described [12 (link)]. Antibodies used for MLX and H3K27ac were anti-MLX (85570 S, Cell Signaling Technology) and anti-H3K27ac (07-360, Millipore), respectively. As for data analysis, FastQC was used for examining the quality of sequenced reads. Reads were then aligned to the human genome hg38 using bowtie2 and duplicated reads were then removed using samtools [26 (link)]. Identification of peaks is carried out by utilizing the “broad peak” calling mode of MACS3 [27 (link)]. DeepTools [28 (link)] was used to create bigwig files and Integrative Genomics Viewer (IGV) [29 (link)] was used for ChIP-seq visualization. Super-enhancer calling was carried out using Ranking of Super Enhancers [6 (link)] and the super-enhancer-associated genes were identified using GREAT [30 (link)].