Advances in Genome-Wide DNA Methylation Analysis

Abstract

The covalent DNA modification of cytosine at position 5 (5-methylcytosine; 5mC) has emerged as an important epigenetic mark most commonly present in the context of CpG dinucleotides in mammalian cells. In pluripotent stem cells and plants, it is also found in non-CpG and CpNpG contexts, respectively. 5mC has important implications in a diverse set of biological processes, including transcriptional regulation. Aberrant DNA methylation has been shown to be associated with a wide variety of human ailments and thus is the focus of active investigation. Methods used for detecting DNA methylation have revolutionized our understanding of this epigenetic mark and provided new insights into its role in diverse biological functions. Here we describe recent technological advances in genome-wide DNA methylation analysis and discuss their relative utility and drawbacks, providing specific examples from studies that have used these technologies for genome-wide DNA methylation analysis to address important biological questions. Finally, we discuss a newly identified covalent DNA modification, 5-hydroxymethylcytosine (5hmC), and speculate on its possible biological function, as well as describe a new methodology that can distinguish 5hmC from 5mC.

Optimizing methodologies for PCR-based DNA methylation analysis

“…Current needs in this field include ( i ) detailed experimental comparisons of results obtained with different PCR-based techniques (72), ( ii ) the availability of a large number of predesigned PCR-based DNA methylation assays to facilitate broad use, ( iii ) the implementation of minimum reporting guidelines for manuscripts describing results of PCR-based analyses of DNA methylation, including details of experimental conditions such as controls, primer sequences, and programs used for primer design (73), ( iv ) the further development of additional PCR-based techniques that allow DNA methylation measurements in a more quantitative and reproducible way (5), and ( v ) the implementation of automatic and multiplexed protocols for DNA methylation using currently available techniques to improve efficiency and reduce costs (59). For readers interested in genome-wide DNA methylation analysis, we recommend two available review articles (74,75). Finally, it is critical to keep in mind that the results of PCR-based DNA methylation methodologies are reliable only in an experimental setting with adequate methodological controls.…”

Changes in methylation of genomic DNA from chicken immune organs in response to H5N1 influenza virus infection

“…A number of detection methods have been developed over the past decade (Shiraishi et al, 2004;Suzuki and Bird, 2008;Gupta et al, 2010;Mastan et al, 2012;Shan et al, 2012). F-MSAP is a technique used to detect DNA methylation at the whole-genome level.…”

α-Lipoic acid attenuates LPS-induced liver injury by improving mitochondrial function in association with GR mitochondrial DNA occupancy

“…DNA methylation is associated with almost every biological process, including repression of transcription and maintenance of genomic stability [46]. In the mitochondrial genome, the D-loop is a non-coding region within mtDNA (NC_005089.1) that is required for replication and transcription of mtDNA [39].…”