# Epigenetic Signatures of Dental Stem Cells: Insights into DNA Methylation and Noncoding RNAs
## 4 Discussion
DANCR inhibits osteogenic differentiation and it enhances TNF-\(\alpha\)/IL-6-mediated osteoclastogenesis in PDLSCs [23; 24]. MIR22 HG, a long noncoding RNA that also hosts the microRNA has-mir-22, was upregulated during the osteogenic differentiation of human PDLSCs. This upregulation closely mirrored the expression of osteogenic genes, suggesting their potential role in promoting osteogenesis [25]. Its role in alveolar bone regeneration has also been reported in in vivo studies [26]. ZFAS1 promotes osteogenesis by regulating the miR-499/EPHA5 axis and participates in the epigenetic control of osteogenic pathways [27]. MALAT1 is involved in both osteoblast and osteoclast regulation, modulates osteogenic differentiation through the miR-204/Smad4 axis [28], and regulates osteoclast activity by modulating the RANKL/OPG ratio and NF-\(\kappa\)B signaling [29], which are mechanisms critical to alveolar bone turnover. The consistent methylation patterns observed at these loci suggest a possible shared regulatory mechanism across dental stem cell types. This is particularly relevant in the context of dental cell identity and differentiation, where epigenetic regulation of noncoding elements is increasingly recognized as a critical layer of control [42]. These findings support emerging evidence that lncRNAs are key epigenetic and transcriptional regulators in odontogenesis [22; 43; 44] and orthodontic bone remodeling. Furthermore, network analysis based on coding genes with shared promoters with noncoding elements revealed the occurrence of genes previously associated with odontogenesis and dental anomalies. These genes contribute to processes such as epithelial signaling (_WNT2_, _PITX2_) [45; 46], tooth morphogenesis (_GL13_) [47], tissue mineralization (_BMP2_) [48], _BMP7_ [49], and lamina positioning (_PITX2_) [50]. Others, such as _GATA2_ [51] and _OSR2_ [52], have been found to play a role in both normal odontogenesis and dental malformations. This result reinforces the biological relevance of the methylation-defined pathways and highlights the potential of this network-based approach to uncover novel regulatory elements involved in tooth development, including those among noncoding elements. Moreover, the presence of known odontogenic regulators within the network supports its use as a discovery tool to prioritize additional candidates, both coding and noncoing, for functional validation in dental biology, regenerative medicine applications, and orthodontics applications. Several previous studies focused on methylation changes during differentiation in cell types--such as DPSCs or PDLSCs--[40,41,53]. Compared to previous studies on DNA methylation in odontogenic stem cells, this work adopts a broad and integrative perspective. The study on which the present analyses are based [8] provided initial evidence that differential methylation profiles among dental pulp stem cells (DPSCs), periodontal ligament stem cells (PDLSCs), and dental follicle progenitor cells (DFPCs) are associated with their distinct osteogenic capacities, with PDLSCs exhibiting superior bone-forming potential. Their analysis focused primarily on identifying differentially methylated CpG sites linked to osteogenesis, followed by functional validation in vitro and in vivo, without exploring the broader regulatory epigenomic context or the contribution of noncoding RNAs [8]. In this study, a publicly available dataset (GSE112933), was reanalyzed, using an updated, stringent bioinformatic pipeline. A high-confidence probe filtering, CpG-context classification, and variance-based clustering were applied to uncover six distinct methylation clusters, each linked to specific biological processes via GO and KEGG enrichment. Crucially, a novel layer of analysis was incorporated, focusing on noncoding RNAs associated with consistently methylated promoter regions. By constructing a gene-concept regulatory network, central transcriptional regulators that are implicated in tooth development and dental anomalies were identified.