MeLncTRN

Epigenetic modifications, such as DNA methylation and histone modication, affect many aspects of chromosomal biology, primarily including regulation of genes by remodeling broad chromatin domains. While it has been known that RNA is an integral component of chromatin, it is only recently that we are beginning to appreciate the means by which Long noncoding RNAs (LncRNAs) is involved in pathways of chromatin modification.

Here, we proposed an integrated framework MeLncTRN (DNA Methylation mediated LncRNA Transcriptional Regulatory Network) to systematic dissection of lncRNA mediated DNA methylation pertubations and associated transcriptional dysregulation in 18 types of cancer. Our analysis indicated that transcriptional alterations are widely mediated by lncRNAs via regulation of genome wide DNA methylation in cancers. Analysis across different cancers reveals four distinct types of regulatory mode between lncRNA modulators and target genes. In addition, lncRNA mediated DNA methylation pertubation may occurs in different types of cancer, in which the lncRNA modulators could paly a role in pan-cancer or cancer speicific mode. Functional studies indicated these lncRNA modulators may involved in a wide spectrum of biological processes. Furthermore, we identified many lncRNA modulators with potential biomedical significance, which show differentially expressed in cancer or are strongly correlated patient survival. This database was constructed for exploring the lncRNA mediated DNA methylation perturbations and associated transcriptional dysregulation across cancer types. This platform presents a valuable tool and resource for investigating the function of lncRNAs in cancer.