IR@PKUHSC  > 北京大学临床肿瘤学院
学科主题临床医学
Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas
Xiang, Shengyan; Liu, Zhaojun; Zhang, Baozhen; Zhou, Jing; Zhu, Bu-Dong; Ji, Jiafu; Deng, Dajun
刊名BMC CANCER
2010-02-17
DOI10.1186/1471-2407-10-44
10
收录类别SCI
文章类型Article
WOS标题词Science & Technology
类目[WOS]Oncology
资助者National Basic Research Program of China ; National High Technology RD Program ; Beijing Natural Science Foundation ; National Basic Research Program of China ; National High Technology RD Program ; Beijing Natural Science Foundation
研究领域[WOS]Oncology
关键词[WOS]PERFORMANCE LIQUID-CHROMATOGRAPHY ; DNA METHYLATION ; CANCER ; TUMORS ; CELLS ; HYPERMETHYLATION ; REPEATS ; ISLANDS ; LINE-1 ; RNA
英文摘要

Background: Alu 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.

Methods: Bisulfite 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.

Results: From 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 similar to 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%).

Conclusions: Most 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.

语种英语
所属项目编号2010CB529303 ; 2006AA02A402 ; 7082022
资助者National Basic Research Program of China ; National High Technology RD Program ; Beijing Natural Science Foundation ; National Basic Research Program of China ; National High Technology RD Program ; Beijing Natural Science Foundation
WOS记录号WOS:000275573900001
Citation statistics
Cited Times:20[WOS]   [WOS Record]     [Related Records in WOS]
文献类型期刊论文
条目标识符http://ir.bjmu.edu.cn/handle/400002259/61291
Collection北京大学临床肿瘤学院
作者单位Peking Univ, Sch Oncol, Beijing Canc Hosp & Inst, Key Lab Carcinogenesis & Translat Res,Minist Educ, Beijing 100142, Peoples R China
Recommended Citation
GB/T 7714
Xiang, Shengyan,Liu, Zhaojun,Zhang, Baozhen,et al. Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas[J]. BMC CANCER,2010,10.
APA Xiang, Shengyan.,Liu, Zhaojun.,Zhang, Baozhen.,Zhou, Jing.,Zhu, Bu-Dong.,...&Deng, Dajun.(2010).Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas.BMC CANCER,10.
MLA Xiang, Shengyan,et al."Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas".BMC CANCER 10(2010).
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