title: Whole genome DNA methylation analysis based on high throughput sequencing technology.
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 3gigabases (Gbp) 45bp paired-end MeDIP-seq or MBD-seq uniquely mapped reads is the minimum requirement and cost-effective strategy for methylome pattern analysis.
authors.affiliation: Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.forename: Mingzhi
authors.initials: M
authors.lastname: Ye
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Zhixiang
authors.initials: Z
authors.lastname: Yan
authors.forename: Lee M
authors.initials: LM
authors.lastname: Butcher
authors.forename: Jihua
authors.initials: J
authors.lastname: Sun
authors.forename: Xu
authors.initials: X
authors.lastname: Han
authors.forename: Quan
authors.initials: Q
authors.lastname: Chen
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D000911:Antibodies, Monoclonal / Q000276:immunology; D004247:DNA / Q000737:chemistry / Q000276:immunology / Q000378:metabolism; D019175:DNA Methylation; D015894:Genome, Human / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods; D007963:Leukocytes, Mononuclear / Q000737:chemistry; D008297:Male; D051783:Methyl-CpG-Binding Protein 2 / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D013447:Sulfites / Q000737:chemistry
chemical_list: D000911:Antibodies, Monoclonal; D051783:Methyl-CpG-Binding Protein 2; D013447:Sulfites; D004247:DNA; C009279:sodium bisulfite