title: Sequencing the cancer methylome.
abstract: DNA methylation is the most studied epigenetic event in cancer, with focus being placed on studying the entire DNA methylation landscape in specific cancers. Due to the recent advances of next-generation sequencing technology, several effective methods have been developed for high-throughput analysis of DNA methylation, enabling DNA methylation markers to be innovative diagnostic and therapeutic strategies in cancer. In this review, we discuss various current and emerging technologies in DNA methylation analysis that integrate next-generation sequencing with the basic principles of methylation detections including methylation sensitive restriction enzyme digestion, affinity purification with antibody or binding proteins, and bisulfite treatment. Variations to these described methods have also allowed for detection of 5-hydroxymethylcytosine marks on a genome-wide scale. We also describe several of the bioinformatic tools used to properly analyze methylome-sequencing data. Finally, recently developed artificial transcription-factor (ATF) targeting tools may provide flexible manipulation of DNA methylation events in specific gene regions, revealing the functional consequences of particular DNA methylation events.
authors.affiliation: GRU Cancer Center, Georgia Regents University, Augusta, GA, 30912, USA.
authors.forename: Austin Y
authors.initials: AY
authors.lastname: Shull
authors.forename: Satish K
authors.initials: SK
authors.lastname: Noonepalle
authors.forename: Eun-Joon
authors.initials: EJ
authors.lastname: Lee
authors.forename: Jeong-Hyeon
authors.initials: JH
authors.lastname: Choi
authors.forename: Huidong
authors.initials: H
authors.lastname: Shi
mesh_terms: D000818:Animals; D019175:DNA Methylation; D057890:Epigenomics / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D015183:Restriction Mapping; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites / Q000494:pharmacology
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite