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Methods Mol Biol. 2018;1766:15-29. doi: 10.1007/978-1-4939-7768-0_2.

Biochemical Identification of Nonmethylated DNA by BioCAP-Seq.

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Department of Chemical and Systems Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK.
Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.


CpG islands are regions of vertebrate genomes that often function as gene regulatory elements and are associated with most gene promoters. CpG island elements usually contain nonmethylated CpG dinucleotides, while the remainder of the genome is pervasively methylated. We developed a biochemical approach called biotinylated CxxC affinity purification (BioCAP) to unbiasedly isolate regions of the genome that contain nonmethylated CpG dinucleotides. The resulting highly pure nonmethylated DNA is easily analyzed by quantitative PCR to interrogate specific loci or via massively parallel sequencing to yield genome-wide profiles.


Biotinylated CxxC affinity purification; CpG island; DNA methylation; Nonmethylated DNA; Nonmethylated island

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