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

Neil P Blackledge, Hannah K Long, Jin C Zhou, Skirmantas Kriaucionis, Roger Patient, Robert J Klose

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.

Original languageEnglish
Pages (from-to)e32
JournalNucleic Acids Research
Volume40
Issue number4
DOIs
Publication statusPublished - 10 Dec 2011

Keywords / Materials (for Non-textual outputs)

  • Biotinylation
  • Chromatography, Affinity/methods
  • CpG Islands
  • DNA/isolation & purification
  • DNA Methylation
  • High-Throughput Nucleotide Sequencing
  • Sequence Analysis, DNA
  • Zinc Fingers

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