title: Semiconductor-based sequencing of genome-wide DNA methylation states.
abstract: Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used approach to study DNA methylation genome-wide. Here, we developed a MeDIP-Seq protocol compatible with the Ion Torrent semiconductor-based sequencing platform that is low cost, rapid, and scalable. We applied this protocol to demonstrate MeDIP-Seq on the Ion Torrent platform provides adequate coverage of CpG cytosines, the methylation states of which we validated at single-base resolution on the Infinium HumanMethylation450 BeadChip array, and accurately identifies sites of differential DNA methylation. Furthermore, we applied an integrative approach to further investigate and confirm the role of DNA methylation in alternative splicing and to profile 5mC and 5hmC variants of DNA methylation in normal human brain tissue that is localized over distinct genomic regions. These applications of MeDIP-Seq on the Ion Torrent platform have broad utility and add to the current methodologies for profiling genome-wide DNA methylation states in normal and disease conditions.
authors.affiliation: a Department of Native Hawaiian Health; John A. Burns School of Medicine ; University of Hawaii ; Honolulu , HI USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Corley
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.forename: Xin
authors.initials: X
authors.lastname: Zheng
authors.forename: Annette
authors.initials: A
authors.lastname: Lum-Jones
authors.forename: Alika K
authors.initials: AK
authors.lastname: Maunakea
mesh_terms: D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics; D019175:DNA Methylation; D016678:Genome; D045325:HCT116 Cells; D006801:Humans; D012326:RNA Splicing; D012666:Semiconductors; D017422:Sequence Analysis, DNA / Q000379:methods*; D000097584:DNA Methyltransferase 3B
chemical_list: D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; D000097584:DNA Methyltransferase 3B
keywords: DNA methylation; HCT116; Ion Torrent sequencing; brain; hydroxymethylation; splicing