Long non-coding RNAs (lncRNAs) comprise different species of RNA which exceed 200 nucleotides that are not usually translated into proteins (limited protein-coding capacity) [
1]. They modulate the gene expression at various levels, including transcriptional, post-transcriptional, and epigenetic processing [
2,
3]. Additionally, growing evidence has revealed that lncRNAs could play an important role in various cancers by regulating oncogenes or tumor-suppressors, or even harboring oncogenic and tumor-suppressing effects, representing a new class of cancer biomarkers and therapeutic targets [
4‐
8]. Dysregulation of lncRNAs normally affects cellular functions such as apoptosis resistance, cell proliferation, tumor suppressor evasion, metastasis promotion, and angiogenesis activation in tumorigenesis [
9‐
11], reported in breast cancer [
12], glioblastoma [
13], liver cancer [
14], leukemia [
15], colorectal cancer (CRC) [
6] and several other cancers [
16]. Their expression and function can be influenced by mutation [
17] or epigenetic changes, including DNA methylation [
8]. Epigenetic modifications have key roles in cancer biology and cell growth [
18‐
20]. Recent studies of DNA methylation analysis in tumor cells have identified several thousand differential methylated regions (DMRs) [
21] with less than 3% mapped to promoters. The majority of DMRs are found in introns or intergenic regions [
22]. It is widely known that tumor cells display global demethylation of intergenic regions expressing large hypomethylation across different types of tumors [
21,
23‐
25]. Of note, one potential function of intergenic DMRs is to regulate the non-coding RNA (ncRNA) expression [
22]. It is predicted that more than 35,000 ncRNA especially lncRNA are positioned at the intergenic regions [
26]. Emerging research indicates that one of the key pathways controlling lncRNA expression and tissue specificity is epigenetic regulation [
27,
28]. Similar to germline genetic mutations, constitutive aberrant methylation may serve as the first hit (according to Knudson’s model of tumor development) in patients with cancer [
29] especially at the intergenic regions. Changes in methylation could be due to single CpG methylation errors at different positions [
30].
We have previously suggested an algorithm to identify methylated CpG sites (accessible in GitHub through the following link:
https://github.com/Genetics-Research-Laboratory-RROC/Candidate_Primer_Region_Finder) using methylation-sensitive high resolution melting (MS-HRM), on data from methylation next-generation sequencing (mNGS). It is feasible that methylation aberrations in crucial single CpG sites could impact the function of the lncRNA similar to single nucleotide polymorphisms (SNPs) of lncRNAs, leading to different impacts on its expression and function [
31‐
33]. Therefore, in this article based on the intergenic position of lncRNAs and single CpG site methylation, an approach for novel lncRNA discovery linked to tumorigenesis is suggested. The newly discovered lncRNA would be attributed to the analyzed cancer type. Furthermore, we used bioinformatics tools and laboratory experiments to identify and validate the novel lncRNAs.