CellMethy: Identification of a focal concordantly methylated pattern of CpGs revealed wide differences between normal and cancer tissues
| Autor: | Yan Zhang, Yihan Wang, Hongbo Liu, Jianzhong Su, Yanjun Wei, Dongwei Zhang, Fang Wang, Xiaole Han, Baodong Xie, Shaojun Zhang |
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| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Multidisciplinary
Bisulfite sequencing Cancer Methylation Hep G2 Cells Biology DNA Methylation medicine.disease Molecular biology Article Jurkat Cells Epigenetics of physical exercise Differentially methylated regions CpG site Cell Line Tumor Neoplasms DNA methylation medicine Humans CpG Islands K562 Cells RNA-Directed DNA Methylation |
| Zdroj: | Scientific Reports |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/srep18037 |
| Popis: | DNA methylation patterns may serve as a key in determining cell phenotypes and functions. Adjacent CpG patterns may provide insight into methylation functional mechanisms. Some regions display different DNA methylation patterns between normal and cancer tissues, but the same average methylation level. Here, we developed a method (CellMethy) to infer a region in which all CpGs exhibit concordant methylation (CM) and to quantify the extent of CM in the region. Using simulation data, CellMethy showed high performance in discovering the concordant methylation patterns (AUC = 0.89). CellMethy was then applied to RRBS data including 11 normal tissues and 12 tumors. We found that the extent of CM exhibited wider differentials among tissues than did the average methylation levels from the CM regions, with 45% of CM regions occurring specifically in one tissue and mainly in tumors. Then, we identified CM regions through genome wide bisulfite sequencing (GWBS) data on breast cancer. Approximately 82% of CM regions revealed a significantly different extent of CM between cancer and normal tissues. CellMethy can accurately describe concordantly methylated regions and the results suggest that CM might also serve as a stable marker of cell sub-populations. |
| Databáze: | OpenAIRE |
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