Identification of long non-coding RNA using single nucleotide epimutation analysis: a novel gene discovery approach

BACKGROUND: Long non-coding RNAs (lncRNAs) are involved in a variety of mechanisms related to tumorigenesis by functioning as oncogenes or tumor-suppressors or even harboring oncogenic and tumor-suppressing effects; representing a new class of cancer biomarkers and therapeutic targets. It is predicted that more than 35,000 ncRNA especially lncRNA are positioned at the intergenic regions of the human genome. Emerging research indicates that one of the key pathways controlling lncRNA expression and tissue specificity is epigenetic regulation. METHODS: In the current article, a novel approach for lncRNA discovery based on the intergenic position of most lncRNAs and a single CpG site methylation level representing epigenetic characteristics has been suggested. RESULTS: Using this method, a novel antisense lncRNA named LINC02892 presenting three transcripts without the capacity of coding a protein was found exhibiting nuclear, cytoplasmic, and exosome distributions. CONCLUSION: The current discovery strategy could be applied to identify novel non-coding RNAs influenced by methylation aberrations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12935-022-02752-2.