EphrinA5 regulates cell motility by modulating lncRNA/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter

Background: Cell-cell communication is mediated by membrane receptors and their cognate ligands, such as the Eph/ephrin system, and dictates physiological processes, including cell proliferation and migration. However, whether and how Eph/ephrin signaling culminates in transcriptional regulation is largely unknown. Epigenetic mechanisms are key for integrating external “signals”, e.g., from neighboring cells, into the transcriptome. We have previously reported that ephrinA5 stimulation of immortalized cerebellar granule (CB) cells elicits transcriptional changes of lncRNAs and protein-coding genes. LncRNAs represent important adaptors for epigenetic writers through which they regulate gene expression. Hence, we here aimed to investigate, whether ephrinA5 can act on gene transcription through modulating lncRNA-mediated targeting of the DNA methyltransferase 1 (DNMT1) to gene promoters, thereby regulating cell motility. Results: We analyzed the interaction of lncRNA with protein-coding genes by the combined power of in silico modeling of RNA/DNA interactions and respective wet lab approaches. We found that Snhg15 , a cancer-related lncRNA, forms a triplex structure with the Ncam1 promoter and interacts with DNMT1. EphrinA5 stimulation leads to reduced Snhg15 expression, diminished Snhg15 /DNMT1 interaction and decreased DNMT1 association with the Ncam1 promoter. These findings can explain the attenuated Ncam1 promoter methylation and elevated Ncam1 expression induced by ephrinA5 stimulation that in turn elicits decreased cell motility of CB cells. Conclusion: Based on our findings, we propose that ephrinA5 influences gene transcription via lncRNA-targeted DNA methylation underlying the regulation of cellular motility. Such mechanism could be relevant in the context of cancerogenic processes, known to involve Eph/ephrin signaling and epigenetic remodelling.