title: Single-base resolution analysis of DNA epigenome via high-throughput sequencing.
abstract: Epigenetic changes caused by DNA methylation and histone modifications play important roles in the regulation of various cellular processes and development. Recent discoveries of 5-methylcytosine (5mC) oxidation derivatives including 5-hydroxymethylcytosine (5hmC), 5-formylcytsine (5fC) and 5-carboxycytosine (5caC) in mammalian genome further expand our understanding of the epigenetic regulation. Analysis of DNA modification patterns relies increasingly on sequencing-based profiling methods. A number of different approaches have been established to map the DNA epigenomes with single-base resolution, as represented by the bisulfite-based methods, such as classical bisulfite sequencing (BS-seq), TAB-seq (TET-assisted bisulfite sequencing), oxBS-seq (oxidative bisulfite sequencing) and etc. These methods have been used to generate base-resolution maps of 5mC and its oxidation derivatives in genomic samples. The focus of this review will be to discuss the chemical methodologies that have been developed to detect the cytosine derivatives in the genomic DNA.
authors.affiliation: State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. jypengpku@pku.edu.cn.
authors.forename: Jinying
authors.initials: J
authors.lastname: Peng
authors.affiliation: State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Xia
authors.affiliation: State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. chengqi.yi@pku.edu.cn.|Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. chengqi.yi@pku.edu.cn.
authors.forename: Chengqi
authors.initials: C
authors.lastname: Yi
mesh_terms: D000818:Animals; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000639:trends*; D016678:Genome / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: DNA methylation; TAB-seq; bisulfite sequencing (BS-Seq); epigenetics; fC-CET; oxBS-seq