Comprehensive analysis of epigenetic pattern of long noncoding RNA loci in colorectal cancer

Colorectal cancer (CRC) is one of the most common and severe cancers worldwide. The occurrence of CRC is developed by accumulation of genetic and epigenetic alteration in colon cells. Work over the last decade has proposed that epigenetic changes such as DNA methylation, histone modification of protein coding genes play an important role in CRC development. However, the epigenetic pattern and features of lncRNAs in CRC were unclear. Here, we comprehensively analyze the patterns of DNA methylation, H3K4me3, H3K27me3 on both protein coding genes and lncRNAs. We found several interesting results which may help to discriminate the lncRNAs from protein coding genes. For example, the signals of DNA methylation and H3K4me3 are higher on protein coding genes than lncRNAs, but not for H3K27me3; the three epigenetic marks show different distribution on promoters, termination and across the whole gene between protein coding genes and lncRNAs, especially DNA methylation, which show regular signal tendency according to the principle of gene transcription. In addition, we further analyzed the affections of epigenetic marks on protein coding gene and lncRNA expression in HCT116 colon cell. Most of the results were consistent with the previous reports such as H3K27me3 is an repressive mark. Furthermore, we analyzed the relationships among the three epigenetic marks and found that DNA methylation and H3K4me3 were positively correlated in promoter and termination region for both protein coding genes and lncRNAs. In a word, our results will give a clue to further study the pathologies of CRC.