Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4

Background: Myeloid differentiation gives rise to a plethora of immune cells in the human body. This differentiation leaves strong signatures in the epigenome through each differentiated state of genetically identical cells. The leukemic HL-60/S4 promyelocytic cell can be easily differentiated from its undifferentiated promyelocyte state into neutrophil- and macrophage-like cell states, making it an excellent system for studying myeloid differentiation. In this study, we present the underlying genome and epigenome architecture of HL-60/S4 through its undifferentiated and differentiated cell states. Results: We performed whole genome bisulphite sequencing of HL-60/S4 cells and their differentiated counterparts. With the support of karyotyping, we show that HL-60/S4 maintains a stable genome throughout differentiation. Analysis of differential CpG methylation reveals that most methylation changes occur in the macrophage-like state. Differential methylation of promoters was associated with immune related terms. Key immune genes, CEBPA, GFI1, MAFB and GATA1 showed differential expression and methylation. However, we observed strongest enrichment of methylation changes in enhancers and CTCF binding sites, implying that methylation plays a major role in large scale transcriptional reprogramming and chromatin reorganisation during differentiation. Correlation of differential expression and distal methylation with support from chromatin capture experiments allowed us to identify putative proximal and long-range enhancers for a number of immune cell differentiation genes, including CEBPA and CCNF. Integrating expression data, we present a model of HL-60/S4 differentiation in relation to the wider scope of myeloid differentiation. Conclusions: For the first time, we elucidate the genome and CpG methylation landscape of HL-60/S4 during differentiation. We identify all differentially methylated regions and positions. We link these to immune function and to important factors in myeloid differentiation. We demonstrate that methylation plays a more significant role in modulating transcription via enhancer reprogramming, rather than by promoter regulation. We identify novel regulatory regions of key components in myeloid differentiation that are regulated by differential methylation. This study contributes another layer of 9omics characterisation of the HL-60/S4 cell line, making it an excellent model system for studying rapid in vitro cell differentiation.