Profiling DNA Methylation Patterns of Non-coding RNAs (ncRNAs) in Human Disease

Although non-coding RNAs (ncRNAs) are commonly considered modulators in human disease, revealing the methylation pattern of ncRNA is still a challenging task. In this chapter, we (1) introduced a strategy of constructing DNA methylation profiles for ncRNAs by reannotating data of DNA methylation arrays; (2) identified methylation patterns of ncRNAs in cancers by classifying ncRNAs into two categories and three subcategories, according to their promoter methylation patterns in tumors; (3) identified lncRNAs with promoter methylation patterns that were associated with cancer status, subtype, or prognosis for several cancers by integrating cancer subtype data and patient clinical information; Furthermore, a panel of ncRNAs were identified as biomarkers that discriminated between disease phenotypes. The potential functions of aberrantly methylated ncRNAs were predicted, suggesting that ncRNAs and coding genes cooperatively mediate pathway dysregulation during the development and progression of breast cancer.