Journal
METHODS
Volume 52, Issue 3, Pages 203-212Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ymeth.2010.04.009
Keywords
DNA methylation; Bisulfite-sequencing; MeDIP-sequencing; MBD-sequencing
Funding
- National Natural Science Foundation of China [30890032]
- Chinese 863 program [2006AA10A121]
- Chinese Academy of Science [GJHZ0701-6]
- Shenzhen Bureau of Science Technology & Information, China [JC200903190772A, JC200903190774A, JC200903190767A, CXB200903110066A, ZYC200903240080A, ZYC200903240077A]
- Danish Platform for Integrative Biology
- Danish Natural Science Research Council
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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. (C) 2010 Elsevier Inc. All rights reserved.
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