Whole genome DNA methylation analysis based on high throughput sequencing technology

Li, Ning, Ye, Mingzhi, Li, Yingrui, Yan, Zhixiang, Butcher, Lee M., Sun, Jihua, Han, Xu, Chen, Quan, Zhang, Xiuqing and Wang, Jun (2010) Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods, 52 3: 203-212. doi:10.1016/j.ymeth.2010.04.009

Author Li, Ning
Ye, Mingzhi
Li, Yingrui
Yan, Zhixiang
Butcher, Lee M.
Sun, Jihua
Han, Xu
Chen, Quan
Zhang, Xiuqing
Wang, Jun
Title Whole genome DNA methylation analysis based on high throughput sequencing technology
Journal name Methods   Check publisher's open access policy
ISSN 1046-2023
Publication date 2010-11
Sub-type Article (original research)
DOI 10.1016/j.ymeth.2010.04.009
Open Access Status Not yet assessed
Volume 52
Issue 3
Start page 203
End page 212
Total pages 10
Place of publication Maryland Heights, MO, United States
Publisher Academic Press
Language eng
Abstract There are numerous approaches to decipher a whole genome DNA methylation profile ("methylome" ), each varying in cost, throughput and resolution. The gold standard of these methods, whole genome bisulfite-sequencing (BS-seq), involves treatment of DNA with sodium bisulfite combined with subsequent high throughput sequencing. Using BS-seq, we generated a single-base-resolution methylome in human peripheral blood mononuclear cells (in press). This BS-seq map was then used as the reference methylome to compare two alternative sequencing-based methylome assays (performed on the same donor of PBMCs): methylated DNA immunoprecipitation (MeDIP-seq) and methyl-binding protein (MBD-seq). In our analysis, we found that MeDIP-seq and MBD-seq are complementary strategies, with MeDIP-seq more sensitive to highly methylated, high-CpG densities and MDB-seq more sensitive to highly methylated, moderate-CpG densities. Taking into account the size of a mammalian genome and the current expense of sequencing, we feel 3. gigabases (Gbp) 45. bp paired-end MeDIP-seq or MBD-seq uniquely mapped reads is the minimum requirement and cost-effective strategy for methylome pattern analysis.
Keyword Bisulfite-sequencing
DNA methylation
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 72 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 90 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Fri, 04 Sep 2015, 11:46:39 EST by Mr Mathew Carter on behalf of Scholarly Communication and Digitisation Service