Biochemical Identification of Nonmethylated DNA by BioCAP-Seq

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

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.

Keywords: Biotinylated CxxC affinity purification; CpG island; DNA methylation; Nonmethylated DNA; Nonmethylated island.

MeSH terms

  • Animals
  • Biotinylation
  • CpG Islands / genetics*
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism*
  • DNA Methylation*
  • F-Box Proteins / chemistry
  • F-Box Proteins / genetics
  • F-Box Proteins / metabolism*
  • Genetic Loci / genetics
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Jumonji Domain-Containing Histone Demethylases / chemistry
  • Jumonji Domain-Containing Histone Demethylases / genetics
  • Jumonji Domain-Containing Histone Demethylases / metabolism*
  • Mice
  • Promoter Regions, Genetic / genetics
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism*
  • Sequence Analysis, DNA / methods*

Substances

  • F-Box Proteins
  • Recombinant Proteins
  • DNA
  • Jumonji Domain-Containing Histone Demethylases
  • KDM2A protein, human