ArticleBMC cancer2010
Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas.
Article in BMC cancer, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 40 citations in OpenAlex.
- Article
- lncRNA BC200 is processed into a stable Alu monomer.RNA (New York, N.Y.) · 2024Article
- The common bisulfite-conversion-based techniques to analyze DNA methylation in human cancers.Cancer cell international · 2024Review
- Air pollution and pregnancy.Seminars in perinatology · 2023Article
- Review
- Integration of TE Induces Cancer Specific Alternative Splicing Events.International journal of molecular sciences · 2022Review
- AnNAR genomics and bioinformatics · 2022Article
- The L1-dependant and Pol III transcribed Alu retrotransposon, from its discovery to innate immunity.Molecular biology reports · 2021Review
- Methylation-driven model for analysis of dinucleotide evolution in genomes.Theoretical biology & medical modelling · 2020Article
- Diversity of genetic events associated with MLH1 promoter methylation in Lynch syndrome families with heritable constitutional epimutation.Genetics in medicine : official journal of the American College of Medical Genetics · 2018Article
- Alu RNA accumulation induces epithelial-to-mesenchymal transition by modulating miR-566 and is associated with cancer progression.Oncogene · 2018Article
- The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells.Genome research · 2017Article
- Proton Beams Inhibit Proliferation of Breast Cancer Cells by Altering DNA Methylation Status.Journal of Cancer · 2016Article
- Critical evaluation of Cbx7 downregulation in primary colon carcinomas and its clinical significance in Chinese patients.BMC cancer · 2015Article
- Circulating DNA and its methylation level in inflammatory bowel disease and related colon cancer.International journal of clinical and experimental pathology · 2015Article
- Transposable elements in cancer as a by-product of stress-induced evolvability.Frontiers in genetics · 2014Article
- Article
- HERV-K and LINE-1 DNA Methylation and Reexpression in Urothelial Carcinoma.Frontiers in oncology · 2013Article
- Long interspersed nuclear element-1 hypomethylation in cancer: biology and clinical applications.Clinical epigenetics · 2011Article
- Spreading of Alu methylation to the promoter of the MLH1 gene in gastrointestinal cancer.PloS one · 2011Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlu methylation is correlated with the overall level of DNA methylation and recombination activity of the genome. However, the maintenance and methylation status of each CpG site within Alu elements (Alu) and its methylation status have not well characterized. This information is useful for understanding natural status of Alu in the genome and helpful for developing an optimal assay to quantify Alu hypomethylation.
methodsBisulfite clone sequencing was carried out in 14 human gastric samples initially. A Cac8I COBRA-DHPLC assay was developed to detect methylated-Alu proportion in cell lines and 48 paired gastric carcinomas and 55 gastritis samples. DHPLC data were statistically interpreted using SPSS version 16.0.
resultsFrom the results of 427 Alu bisulfite clone sequences, we found that only 27.2% of CpG sites within Alu elements were preserved (4.6 of 17 analyzed CpGs, A approximately Q) and that 86.6% of remaining-CpGs were methylated. Deamination was the main reason for low preservation of methylation targets. A high correlation coefficient of methylation was observed between Alu clones and CpG site J (0.963), A (0.950), H (0.946), D (0.945). Comethylation of the sites H and J were used as an indicator of the proportion of methylated-Alu in a Cac8I COBRA-DHPLC assay. Validation studies showed that hypermethylation or hypomethylation of Alu elements in human cell lines could be detected sensitively by the assay after treatment with 5-aza-dC and M.SssI, respectively. The proportion of methylated-Alu copies in gastric carcinomas (3.01%) was significantly lower than that in the corresponding normal samples (3.19%) and gastritis biopsies (3.23%).
conclusionsMost Alu CpG sites are deaminated in the genome. 27% of Alu CpG sites represented in our amplification products. 87% of the remaining CpG sites are methylated. Alu hypomethylation in primary gastric carcinomas could be detected with the Cac8I COBRA-DHPLC assay quantitatively.
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