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CpG Islands pp 15-29 | Cite as

Biochemical Identification of Nonmethylated DNA by BioCAP-Seq

  • Hannah K. Long
  • Nathan R. Rose
  • Neil P. Blackledge
  • Robert J. Klose
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1766)

Abstract

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.

Key words

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

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Hannah K. Long
    • 1
    • 2
    • 3
  • Nathan R. Rose
    • 2
  • Neil P. Blackledge
    • 2
  • Robert J. Klose
    • 2
  1. 1.Department of Chemical and Systems Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanford UniversityStanfordUSA
  2. 2.Department of BiochemistryUniversity of OxfordOxfordUK
  3. 3.Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe HospitalUniversity of OxfordOxfordUK

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