Genome-scale DNA methylation analysis

Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, CA 94158, USA.
Epigenomics (Impact Factor: 4.65). 02/2010; 2(1):105-17. DOI: 10.2217/epi.09.35
Source: PubMed


The haploid human genome contains approximately 29 million CpGs that exist in a methylated, hydroxymethylated or unmethylated state, collectively referred to as the DNA methylome. The methylation status of cytosines in CpGs and occasionally in non-CpG cytosines influences protein–DNA interactions, gene expression, and chromatin structure and stability. The degree of DNA methylation at particular loci may be heritable transgenerationally and may be altered by environmental exposures and diet, potentially contributing to the development of human diseases. For the vast majority of normal and disease methylomes however, less than 1% of the CpGs have been assessed, revealing the formative stage of methylation mapping techniques. Thus, there is significant discovery potential in new genome-scale platforms applied to methylome mapping, particularly oligonucleotide arrays and the transformative technology of next-generation sequencing. Here, we outline the currently used methylation detection reagents and their application to microarray and sequencing platforms. A comparison of the emerging methods is presented, highlighting their degrees of technical complexity, methylome coverage and precision in resolving methylation. Because there are hundreds of unique methylomes to map within one individual and interindividual variation is likely to be significant, international coordination is essential to standardize methylome platforms and to create a full repository of methylome maps from tissues and unique cell types.

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    • "One of the best studied DNA damage product, 8-oxo-7,8-dihydroguanine (8-oxoGua), is a marker of oxidative stress, and is formed in DNA via a direct reaction of guanosine with •OH [16], [17]. Potentially, the same random radical reaction can take place with all normal and modified DNA constituents, including 5-methyldeoxycytosine in eukaryotic DNA [8], [9]. It is assumed that ca. 5% of all cytosine residues or 1% of bases in the mammalian genomes are methylated. "
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    • "Moreover, progress in DNA sequencing technologies has allowed the re-sequencing of whole human genomes within a reasonable time and cost (3). The combination of bisulfite-converted DNA with next-generation sequencing (NGS) allows for a powerful whole epigenome analysis (4). "
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    Nucleic Acids Research 01/2013; 41(6). DOI:10.1093/nar/gks1467 · 9.11 Impact Factor
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    • "Experimental methods for detecting DNA methylation have been perfected over many decades [23] [24] [25]. Perhaps the biggest breakthrough in the field came from Hikoya Hiyatsu's discovery that the treatment of DNA with high concentrations of bisulfite results in rapid deamination of cytosine and its conversion to uracil [26]. "
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