title: Profiling genome-wide DNA methylation.
abstract: DNA methylation is an epigenetic modification that plays an important role in regulating gene expression and therefore a broad range of biological processes and diseases. DNA methylation is tissue-specific, dynamic, sequence-context-dependent and trans-generationally heritable, and these complex patterns of methylation highlight the significance of profiling DNA methylation to answer biological questions. In this review, we surveyed major methylation assays, along with comparisons and biological examples, to provide an overview of DNA methylation profiling techniques. The advances in microarray and sequencing technologies make genome-wide profiling possible at a single-nucleotide or even a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, genomic region coverage, and bioinformatics analysis, and selecting a feasible method requires knowledge of these methods. We first introduce the biological background of DNA methylation and its pattern in plants, animals and fungi. We present an overview of major experimental approaches to profiling genome-wide DNA methylation and hydroxymethylation and then extend to the single-cell methylome. To evaluate these methods, we outline their strengths and weaknesses and perform comparisons across the different platforms. Due to the increasing need to compute high-throughput epigenomic data, we interrogate the computational pipeline for bisulfite sequencing data and also discuss the concept of identifying differentially methylated regions (DMRs). This review summarizes the experimental and computational concepts for profiling genome-wide DNA methylation, followed by biological examples. Overall, this review provides researchers useful guidance for the selection of a profiling method suited to specific research questions.
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, ROC.
authors.forename: Wai-Shin
authors.initials: WS
authors.lastname: Yong
authors.affiliation: Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561 Japan.
authors.forename: Fei-Man
authors.initials: FM
authors.lastname: Hsu
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, ROC.
authors.forename: Pao-Yang
authors.initials: PY
authors.lastname: Chen
keywords: Bisulfite sequencing; DNA methylation; Hydroxymethylation; Methylome; RRBS; Single-cell; WGBS