Detailed methylation map of LINE-1 5'-promoter region reveals hypomethylated CpG hotspots associated with tumor tissue specificity
| Autor: | Albertas Daukša, Muhammad Jamil, Antanas Gulbinas, Amit Sharma, Wolfgang A. Schulz, Nicole Nuesgen, Johannes Oldenburg, Osman El-Maarri |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Male Computational biology 030105 genetics & heredity Biology Neoplasms genetics DNA methylation Long interspersed nucleotide elements Biomarkers tumor Promoter regions genetic 03 medical and health sciences Genetics medicine Humans cancer Epigenetics Promoter Regions Genetic Molecular Biology Genetics (clinical) Tumor marker epigenetics Cancer Promoter SIRPH Methylation Original Articles LINE‐1 medicine.disease bisulfite modification 030104 developmental biology Long Interspersed Nucleotide Elements CpG site Organ Specificity tumor marker biomarker Human genome CpG Islands Female Original Article 616-006.6 [udc] methylation patterns |
| Zdroj: | Molecular Genetics & Genomic Medicine Molecular genetics & genomic medicine, Hoboken : Wiley, 2019, vol. 7, no. 5, e601, p. 1-5 |
| ISSN: | 2324-9269 |
| Popis: | Background Long interspersed nuclear elements (LINE‐1) sequences constitute a substantial portion of the human genome, and their methylation often correlating with global genomic methylation. Previous studies have highlighted the feasibility of using LINE‐1 methylation to discriminate tumors from healthy tissues. However, most studies are based on only a few specific LINE‐1 CpG sites. Methods Herein, we have performed a systematic fine‐scale analysis of methylation at 14 CpGs located in the 5′‐region of consensus LINE‐1, in bladder, colon, prostate, and gastric tumor tissues using a global degenerate approach. Results Our results reveal variable methylation levels between different CpGs, as well as some tissue‐specific differences. Trends toward hypomethylation were observed in all tumors types to certain degrees, showing statistically significance in bladder and prostate tumors. Our data points toward the presence of unique LINE‐1 DNA methylation patterns for each tumor type and tissue, indicating that not the same CpGs will be informative for testing in all tumor types. Conclusion This study provides an accurate guide that will help to design further assays that could avoid artifacts and explain the variability of obtained LINE‐1 methylation values between different studies. |
| Databáze: | OpenAIRE |
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