Systemic analysis of osteoblast-specific DNA methylation marks reveals novel epigenetic basis of osteoblast differentiation

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.

Dnmt3b ablation impairs fracture repair through upregulation of Notch pathway

“…In addition to Rbpjκ, we recently identified hypomethylation in Cxcl12 gene in Dnmt3b LOF chondrocytes (20), suggesting Dnmt3b LOF could directly modify DNA methylation pattern in chondrocyte maturation-related genes. Findings from other groups also demonstrated that chondrogenic-and osteogenic-related genes could be regulated via alteration of DNA methylation in promoters (41)(42)(43). We thus speculate Dnmt3b LOF leads to progenitor differentiation defect through a combination of an altered Notch pathway and the alteration of DNA methylation in chondrogenic-and osteogenic-specific genes.…”

Overexpression of DNMT3b target genes during Enteric Nervous System development contribute to the onset of Hirschsprung disease

“…The roles of this DNA methylation remain unclear as well as how these regions are established, maintained, and function. Nevertheless, increasingly more studies are identifying the methylation of these regions as regulators of gene expression 17 .…”

A DNA-Methylated Sight on Autoimmune Inflammation Network across RA, pSS, and SLE

“…Canonical CpG islands have 300–3000 base pairs and have been found in approximately 70% of promoters located near the transcription start site (TSS) of a human gene such as housekeeping gene, tissue-specific gene, and regulator gene [ 21 ]. The methylation in CpG islands, as well as in CpG island-surrounding regions which contain shores and shelves, had strong correlation with the transcription initiation and chromosome configuration [ 22 ] and affected human health [ 23 , 24 ]. Here, we defined the methylated differences across SLE, RA, and pSS with two principles: (i) there are statistical significances in the analyses of DMVs; (ii) in all three disorders, at least one disorder has a differential methylation status that is completely opposite to the other two, namely, if there is a significant hypermethylated site in SLE, then this site must be significantly decreased in the other two diseases.…”