KDM6A binding sites in myeloma cell lines. (A) Immunoblot showing the detection of KDM6A by an HA antibody in ARP-1 cells in which both alleles of endogenous KDM6A were HA tagged using CRISPR-Cas9 gene editing. ARD is a KDM6A-negative control cell line. (B) Overlap of KDM6A binding sites detected by chromatin precipitation of an HA-tagged ARP-1 cell line with anti-HA or anti-KDM6A antibodies. (C) Distribution of KDM6A binding sites in the annotated regions of the genome in the ARP-1 cell line. (D) Distance and orientation between KDM6A binding regions and their closest genes. (E) Dot plot visualization of gene ontology (GO) biological process enrichment analyses of KDM6A-bound genes using the GoShiny v0.77 tool. The size of the dots reflects the number of genes, the length of the line indicates fold enrichment, and color scale indicates false discovery rate. (F) Similarity of KDM6A binding pattern with those of transcription factors found in the Cistrome database (top 20). Each dot represents a different ChIP experiment. (G) Hypergeometric optimization of motif enrichment (HOMER)–identified enriched transcription factor binding motif within regions bound by KDM6A as identified both by KDM6A and HA antibody in ARP-1 cells expressing HA-tagged KDM6A. (H) Genome browser view of the CIITA and NLRC5 locus in ARP-1 cell line replete or knocked out or KO for KDM6A. FDR, false discovery rate; TSS, transcriptional start site.