RNA duplex formation and competing endogenous RNA, proposed as mechanisms in regulating expression of natural antisense transcripts- from hypotheses to potential therapeutic applications

Natural antisense transcripts (NATs) from eukaryotic genes, known as long non-coding RNAs (lncRNAs), are long transcripts that do not encode proteins. NATs play diverse functional roles in regulating the transcription, stability, and translation of protein-coding genes at the epigenetic and post-transcriptional levels. Here, we outline recent studies on NAT-mediated RNA networks and discuss their potential as therapeutic targets across diseases. Interferon-α1 (IFNA1) mRNA expression is regulated by its overlapping antisense transcript IFNA1-AS through IFNA1 mRNA–AS duplex formation, and microRNA-sponging through common microRNA response elements (MREs) as competing endogenous RNAs. The competitive interactions between NATs and mRNA MRE(s) fine-tune mRNA and protein levels. The receptor tyrosine kinase, ephrin type-A receptor 2 (EPHA2) mRNA and its antisense partner (EPHA2-AS) are transcribed from the EPHA2 gene and are overexpressed in breast cancer. EPHA2-AS interacts with EPHA2 mRNA, forming an mRNA–AS duplex that modulates both EPHA2 mRNA and protein levels, potentially contributing to tumorigenesis; hence, it is a potential target for breast cancer treatment. RNA methylation, such as N6-methyladenosine, may also play a role in regulating gene expression in various diseases. NAT-targeted therapeutics, such as synthetic oligonucleotides, mRNA, and drugs, can be introduced into cells either directly or via extracellular vesicles and lipid nanoparticles. The administration of NAT-targeted therapeutics in animal disease models is useful for evaluating their efficacy. The mechanisms of NAT-mediated gene regulation should be further investigated to develop NAT-targeted therapeutics for the treatment of various diseases.