Genome-wide methylation analysis reveals epigenetic remodelling during osteoclastogenesis

Abstract Background Osteoclast differentiation from hematopoietic precursors is essential for bone remodelling and homeostasis. Although the transcriptional programmes controlling osteoclastogenesis are well established, the contribution of DNA methylation to human osteoclast differentiation remains less fully characterised. This study investigated genome-wide DNA methylation changes during human osteoclast differentiation and their relationship with osteoclast-specific gene expression. Results Genome-wide DNA methylation profiling was performed using the Illumina Infinium MethylationEPIC (850k) array to compare osteoclasts differentiated in vitro using receptor activator of NF-κB ligand (RANKL) and macrophage colony-stimulating factor (M-CSF) with their precursors derived from peripheral blood mononuclear cells (PBMCs). Osteoclastogenesis was associated with extensive remodelling of the methylome. Using thresholds of |Δβ| > 0.2 and FDR < 0.05, we identified 9,006 differentially methylated CpG sites (including 8366 hypomethylated and 640 hypermethylated loci) and 1526 differentially methylated regions (DMRs) between the PBMC-derived precursors and osteoclasts. RNA-seq data from matched samples were integrated with the results from the differential methylation analyses to characterise the relationship between DNA methylation and transcriptional regulation. Several key osteoclast genes, including CTSK , OCSTAMP , DCSTAMP , and ATP6V0D2 , exhibited co-ordinated promoter/regulatory-region methylation and gene expression changes consistent with their roles in osteoclast maturation and bone resorption. Motif enrichment analysis identified sequences associated with PU.1 (SPI1), SPI-C, and MYC within hypomethylated regions, suggesting that these transcription factors may contribute to the establishment of osteoclast-specific regulatory programmes. Conclusion Collectively, these findings provide a genome-wide view of DNA methylation remodelling during human osteoclast differentiation and identify epigenetic signatures associated with osteoclast gene activation.