Identification and functional annotation of lncRNA genes with hypermethylation in colorectal cancer

• We identified 761 DNA hypermethylated lncRNAs in CRC by use of a public dataset.
• We mined out 160 significant genome clusters with both hypermethylated protein coding genes and lncRNAs.
• We constructed a coding noncoding gene co-methylation network and annotated the functions of 364 lncRNAs.

Colorectal cancer (CRC) is one of the leading causes of mortality worldwide. DNA methylation is an important epigenetic modification for CRC. Although currently a number of studies about DNA methylation of protein coding genes have been carried out, only a few are about the methylation of genes encoding the long noncoding RNAs (lncRNAs). In this study, we identified 761 lncRNA genes with DNA hypermethylation in CRC using a free MethylCap-seq dataset. Integration of lncRNA expression and methylation datasets showed that the expression of lncRNAs is negatively correlated with DNA methylation (p < 0.01). Co-methylation network was also constructed to annotate the functions of unknown lncRNAs. Our results showed that a total of 364 lncRNAs were annotated with at least one GO biological process term. The current data-mining work is likely to provide informative clues for biological researchers to further understand the role of lncRNAs in the development of CRC.