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Nucleic Acids Res. 2012 Feb;40(4):e32. doi: 10.1093/nar/gkr1207. Epub 2011 Dec 10.

Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA.

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  • 1Department of Biochemistry, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford, UK.

Abstract

Across vertebrate genomes methylation of cytosine residues within the context of CpG dinucleotides is a pervasive epigenetic mark that can impact gene expression and has been implicated in various developmental and disease-associated processes. Several biochemical approaches exist to profile DNA methylation, but recently an alternative approach based on profiling non-methylated CpGs was developed. This technique, called CxxC affinity purification (CAP), uses a ZF-CxxC (CxxC) domain to specifically capture DNA containing clusters of non-methylated CpGs. Here we describe a new CAP approach, called biotinylated CAP (Bio-CAP), which eliminates the requirement for specialized equipment while dramatically improving and simplifying the CxxC-based DNA affinity purification. Importantly, this approach isolates non-methylated DNA in a manner that is directly proportional to the density of non-methylated CpGs, and discriminates non-methylated CpGs from both methylated and hydroxymethylated CpGs. Unlike conventional CAP, Bio-CAP can be applied to nanogram quantities of genomic DNA and in a magnetic format is amenable to efficient parallel processing of samples. Furthermore, Bio-CAP can be applied to genome-wide profiling of non-methylated DNA with relatively small amounts of input material. Therefore, Bio-CAP is a simple and streamlined approach for characterizing regions of the non-methylated DNA, whether at specific target regions or genome wide.

PMID:
22156374
PMCID:
PMC3287171
DOI:
10.1093/nar/gkr1207
[PubMed - indexed for MEDLINE]
Free PMC Article
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