Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2016 Jun 29:9:26.
doi: 10.1186/s13072-016-0075-3. eCollection 2016.

Profiling genome-wide DNA methylation

Wai-Shin Yong #  1 , Fei-Man Hsu #  2 , Pao-Yang Chen  1
Affiliations
Review

Profiling genome-wide DNA methylation

Wai-Shin Yong et al. Epigenetics Chromatin. .

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.

Keywords: Bisulfite sequencing; DNA methylation; Hydroxymethylation; Methylome; RRBS; Single-cell; WGBS.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
Commonly used methods for genome-wide DNA methylation analysis. a The procedures may involve fragmentation of genomic DNA by restriction enzyme digestion or sonication. The genomic DNA can be subjected to MBD enrichment, antibody enrichment, bisulfite conversion or TET oxidation before analyzing by microarray or next-generation sequencing platform. b Single-cell DNA methylation analysis that involves the isolation of single cells allows the assessment of methylation heterogeneity in cell populations while other genome-wide DNA methylation profiling methods using pooled heterogeneous cell populations are not capable to dissect the methylation heterogeneity. Blue concrete dots represent 5mC, and hollowed ones represent C. Each track represents 1 read
Fig. 2
Fig. 2
Schematic overview of genome-wide DNA methylation profiling methods. a 5mC assays. b 5hmC assays. The actual sample requirement may vary according to the type of sample, genome size and number of PCR cycles
Fig. 3
Fig. 3
Computational pipeline for genome-wide bisulfite sequencing data analysis. Reads from bisulfite sequencing are first aligned to the reference genome. The alignment data may be visualized in different tracks for comparison. After methylation calling, the bulk methylation level and genome-wide methylation level are calculated and plotted, and DMRs are determined. To perform an integrative analysis, DNA methylation data are coupled with gene expression, e.g., differentially expressed genes (DEGs), to delineate the regulatory role of DNA methylation
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet. 2013;14:204–220. doi: 10.1038/nrg3354. - DOI - PubMed
    1. Kim KD, El Baidouri M, Jackson SA. Accessing epigenetic variation in the plant methylome. Brief Funct Genomics. 2014;13:318–327. doi: 10.1093/bfgp/elu003. - DOI - PubMed
    1. Berkyurek AC, Suetake I, Arita K, Takeshita K, Nakagawa A, Shirakawa M, et al. The DNA methyltransferase Dnmt1 directly interacts with the SET and RING finger-associated (SRA) domain of the multifunctional protein Uhrf1 to facilitate accession of the catalytic center to hemi-methylated DNA. J Biol Chem. 2014;289:379–386. doi: 10.1074/jbc.M113.523209. - DOI - PMC - PubMed
    1. Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999;99:247–257. doi: 10.1016/S0092-8674(00)81656-6. - DOI - PubMed
    1. Kinde B, Gabel HW, Gilbert CS, Griffith EC, Greenberg ME. Reading the unique DNA methylation landscape of the brain: non-CpG methylation, hydroxymethylation, and MeCP2. Proc Natl Acad Sci USA. 2015;112:6800–6806. doi: 10.1073/pnas.1411269112. - DOI - PMC - PubMed