Long non-coding RNA triplex-dependent regulation of melanoma gene networks

Abstract SLNCR is a long non-coding RNA (lncRNA) that promotes melanoma formation. Previously, we have shown that SLNCR regulates gene expression via its interactions with different transcription factors. Here we show that SLNCR is associated with several genomic sites that contain RNA•DNA triplex target sites (TTSs). The primary sequence of SLNCR contains four triplex-forming regions (TFRs), which are homologous to the TFRs of MEG3, HOTAIR, and PARTICLE lncRNAs. Full-length SLNCR overexpression promotes proliferation, migration, and invasion of melanoma cells by inducing characteristic gene expression changes of genes that are enriched in pathways involved in cell cycle regulation and cell migration. The transcriptomic signature of full-length SLNCR is reversed by deletions of TFR1, 2, 3, or 4. Full-length SLNCR is structurally flexible and permissive of different interactions with the DNA and/or proteins. Deletion of any individual TFR causes SLNCR to gain structural definition, potentially preventing some of its native interactions. Using RNA sequencing and the Triplex Domain Finder tool, we demonstrate that SLNCR TFRs form RNA•DNA:DNA triplexes with the TTSs in promoters of key genes (nodes) predicted to regulate melanoma migration and invasion networks. We further validate the effect on invasion using A375 cells in functional assays. Finally, inhibitory oligos that block SLNCR•DNA:DNA triplex formation reversed the effect of SLNCR-mediated migration ex vivo, demonstrating that triplex formation plays a role in driving melanoma progression.