Genome-wide assays that identify and quantify modified cytosines in human disease studies

Epigenetics & Chromatin
Netha Ulahannan, John M Greally

Abstract

The number of different assays that has been published to study DNA methylation is extensive, complemented by recently described assays that test modifications of cytosine other than the most abundant 5-methylcytosine (5mC) variant. In this review, we describe the considerations involved in choosing how to study 5mC throughout the genome, with an emphasis on the common application of testing for epigenetic dysregulation in human disease. While microarray studies of 5mC continue to be commonly used, these lack the additional qualitative information from sequencing-based approaches that is increasingly recognized to be valuable. When we test the representation of functional elements in the human genome by several current assay types, we find that no survey approach interrogates anything more than a small minority of the nonpromoter cis-regulatory sites where DNA methylation variability is now appreciated to influence gene expression and to be associated with human disease. However, whole-genome bisulphite sequencing (WGBS) adds a substantial representation of loci at which DNA methylation changes are unlikely to be occurring with transcriptional consequences. Our assessment is that the most effective approach to DNA methylation s...Continue Reading

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Methods Mentioned

BETA
PCR
deamination
pull down
immunoprecipitation
ChIP-seq
RRBS
pulldown
genotyping
WGBS

Software Mentioned

ChromHMM
WGBS
Segway
LUMA
Bumphunter

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