Abstract
DNA methylation is an important epigenetic modification that contributes to the lineage commitment and specific functions of different cell types. In this study, we compared ENCODE-generated genome-wide DNA methylation profiles of human osteoblast with 21 other types of human cells in order to identify osteoblast-specific methylation events. For most of the cell strains, data from two isogenic replicates were included, resulting in a total of 51 DNA methylation datasets. We identified 852 significant osteoblast-specific differentially methylated CpGs (DMCs) and 295 significant differentially methylated regions (DMRs). Significant DMCs/DMRs were not enriched in CpG islands (CGIs) and promoters, but more strongly enriched in CGI shores/shelves and in gene body and intergenic regions. The genes associated with significant DMRs were highly enriched in biological processes related to transcriptional regulation and critical for regulating bone metabolism and skeletal development under physiologic and pathologic conditions. By integrating the DMR data with the extensive gene expression and chromatin epigenomics data, we observed complex, context-dependent relationships between DNA methylation, chromatin states, and gene expression, suggesting diverse DNA methylation-mediated regulatory mechanisms. Our results also highlighted a number of novel osteoblast-relevant genes. For example, the integrated evidences from DMR analysis, histone modification and RNA-seq data strongly support that there is a novel isoform of neurexin-2 (NRXN2) gene specifically expressed in osteoblast. NRXN2 was known to function as a cell adhesion molecule in the vertebrate nervous system, but its functional role in bone is completely unknown and thus worth further investigation. In summary, we reported a comprehensive analysis of osteoblast-specific DNA methylation profiles and revealed novel insights into the epigenetic basis of osteoblast differentiation and activity.
Highlights
DNA methylation of cytosine is a crucial epigenetic mechanism for transcriptional regulation and has profound impacts on embryonic development, genomic imprinting, X-chromosome inactivation, and the pathogenesis of various human disorders (Weber et al, 2007)
We compared a total of 182,518 CpGs with coverage ≥10× across all 51 samples and identified 852 significant differentially methylated CpGs (DMCs) with stringent criteria (q b 0.01, difference in methylation ≥ 50%), which were distributed across the entire genome (Supplementary Fig. 1)
We identified and characterized human osteoblastspecific DNA methylation profiles by comparing the genome-wide DNA methylation profiles between human osteoblasts and 21 other types of human cells and by integrating the DNA methylation patterns with transcriptomic and other epigenomic profiles
Summary
DNA methylation of cytosine is a crucial epigenetic mechanism for transcriptional regulation and has profound impacts on embryonic development, genomic imprinting, X-chromosome inactivation, and the pathogenesis of various human disorders (Weber et al, 2007). Though the regulatory function of DNA methylation is generally thought to be associated with transcriptional repression when occurring in gene promoter regions and with transcriptional activation when occurring in gene bodies (Jones, 2012; Ball et al, 2009; Rauch et al, 2009), recent studies revealed a far more complicated relationship between DNA methylation and gene expression. Targeted induction of Trip promoter methylation resulted in reduced Trip expression and accelerated MSC differentiation towards osteogenic lineage at the expense of MSC-to-adipocyte differentiation Taken together, these results strongly supported that DNA methylation plays a significant role in mediating cell-specific gene transcription and interfering with cell fate determination, including osteoblast differentiation
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