Genome-scale DNA methylation analysis.

Epigenomics
Shaun D FouseJoseph F Costello

Abstract

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 ...Continue Reading

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Methods Mentioned

BETA
immunoprecipitation
methylation profiling
PCR
histone acetylation
immunoprecipitation-chip
MeDIP-chip
Assay
size fractionation
MRE-seq
Illumina sequencing

Software Mentioned

MeDIP
CashX
CHARM
Infinium
Batman
Bayesian tool for methylation analysis ( BATMAN )
HELP
GoldenGate

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