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CpG Islands pp 15–29Cite as

Biochemical Identification of Nonmethylated DNA by BioCAP-Seq

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Part of the book series: Methods in Molecular Biology ((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.

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Author information

Authors and Affiliations

  1. 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

    Hannah K. Long

  2. Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK

    Hannah K. Long, Nathan R. Rose, Neil P. Blackledge & Robert J. Klose

  3. Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK

    Hannah K. Long

Authors
  1. Hannah K. Long
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  2. Nathan R. Rose
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  3. Neil P. Blackledge
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  4. Robert J. Klose
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Corresponding author

Correspondence to Robert J. Klose .

Editor information

Editors and Affiliations

  1. Josep Carreras Leukaemia, Research Institute, Badalona, Barcelona, Spain

    Tanya Vavouri

  2. IGTP, IMPPC, Badalona, Barcelona, Spain

    Miguel A. Peinado

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Long, H.K., Rose, N.R., Blackledge, N.P., Klose, R.J. (2018). Biochemical Identification of Nonmethylated DNA by BioCAP-Seq. In: Vavouri, T., Peinado, M. (eds) CpG Islands. Methods in Molecular Biology, vol 1766. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7768-0_2

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  • DOI: https://doi.org/10.1007/978-1-4939-7768-0_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7767-3

  • Online ISBN: 978-1-4939-7768-0

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