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学科主题: 临床医学
题名:
Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas
作者: Xiang, Shengyan; Liu, Zhaojun; Zhang, Baozhen; Zhou, Jing; Zhu, Bu-Dong; Ji, Jiafu; Deng, Dajun
刊名: BMC CANCER
发表日期: 2010-02-17
DOI: 10.1186/1471-2407-10-44
卷: 10
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology
类目[WOS]: Oncology
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
项目资助者: National Basic Research Program of China ; National High Technology RD Program ; Beijing Natural Science Foundation
WOS记录号: WOS:000275573900001
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.bjmu.edu.cn/handle/400002259/61291
Appears in Collections:北京大学临床肿瘤学院_期刊论文

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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:
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.
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