Abstract
ABSTRACTEpigenomic regulation plays a vital role in cell differentiation. The leukemic HL-60/S4 [human myeloid leukemic cell line HL-60/S4 (ATCC CRL-3306)] promyelocytic cell can be easily differentiated from its undifferentiated promyelocyte state into neutrophil- and macrophage-like cell states. In this study, we present the underlying genome and epigenome architecture of HL-60/S4 through its differentiation. 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 Cytosine-phosphate-Guanine dinucleotide 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 the 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.
Highlights
Gene expression profiles differ among different cell types and change as stem cells differentiate (Cheng et al, 1996; Le Naour et al, 2001; Natarajan et al, 2012)
Little or no DNA methylation changes are observed upon HL-60/S4 cell differentiation at the megabase scale We performed whole-genome bisulphite sequencing (WGBS) of HL-60/S4 in three different cell differentiation states: the undifferentiated state (UN), the Retinoic acid (RA)-treated granulocyte state, and the TPA-treated macrophage state
A comparison of HL-60/S4 cells by fluorescent in situ hybridization (FISH) karyotyping showed that this cell line is stable over long time periods (Fig. S1D,E)
Summary
Gene expression profiles differ among different cell types and change as stem cells differentiate (Cheng et al, 1996; Le Naour et al, 2001; Natarajan et al, 2012). Genome-wide Cytosinephosphate-Guanine dinucleotide (CpG) methylation, an epigenetic regulation and modification process, has been shown to exhibit similar dynamic behaviour during differentiation (Brunner et al, 2009; Bock et al, 2012). These two changes (i.e. gene expression and CpG methylation) have been shown to correlate negatively with each other, depending upon the location of the methylated CpG relative to the gene body (Payer and Lee, 2008; Chuang et al, 2012; Jones, 2012; Yang et al, 2014). While CMP cells can differentiate into all myeloid cell types, GMP cells give rise mainly to monocytes/macrophages and neutrophils, together with a minor population of eosinophils, basophils and mast cells (ÁlvarezErrico et al, 2015; Iwasaki and Akashi, 2007; Laiosa et al, 2006)
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