IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v4y2013i1d10.1038_ncomms3190.html
   My bibliography  Save this article

DNA unmethylome profiling by covalent capture of CpG sites

Author

Listed:
  • Edita Kriukienė

    (Institute of Biotechnology, Vilnius University)

  • Viviane Labrie

    (The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health)

  • Tarang Khare

    (The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health)

  • Giedrė Urbanavičiūtė

    (Institute of Biotechnology, Vilnius University)

  • Audronė Lapinaitė

    (Institute of Biotechnology, Vilnius University
    Present address: European Molecular Biology Laboratory, Heidelberg, Germany)

  • Karolis Koncevičius

    (Faculty of Mathematics and Informatics, Vilnius University)

  • Daofeng Li

    (Centre for Genome Sciences and Systems Biology, Washington University School of Medicine)

  • Ting Wang

    (Centre for Genome Sciences and Systems Biology, Washington University School of Medicine)

  • Shraddha Pai

    (The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health)

  • Carolyn Ptak

    (The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health)

  • Juozas Gordevičius

    (Institute of Mathematics and Informatics, Vilnius University)

  • Sun-Chong Wang

    (Institute of Systems Biology and Bioinformatics, National Central University)

  • Artūras Petronis

    (The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health)

  • Saulius Klimašauskas

    (Institute of Biotechnology, Vilnius University)

Abstract

Dynamic patterns of cytosine-5 methylation and successive hydroxylation are part of epigenetic regulation in eukaryotes, including humans, which contributes to normal phenotypic variation and disease risk. Here we present an approach for the mapping of unmodified regions of the genome, which we call the unmethylome. Our technique is based on DNA methyltransferase-directed transfer of activated groups and covalent biotin tagging of unmodified CpG sites followed by affinity enrichment and interrogation on tiling microarrays or next generation sequencing. Control experiments and pilot studies of human genomic DNA from cultured cells and tissues demonstrate that, along with providing a unique cross-section through the chemical landscape of the epigenome, the methyltransferase-directed transfer of activated groups-based approach offers high precision and robustness as compared with existing affinity-based techniques.

Suggested Citation

  • Edita Kriukienė & Viviane Labrie & Tarang Khare & Giedrė Urbanavičiūtė & Audronė Lapinaitė & Karolis Koncevičius & Daofeng Li & Ting Wang & Shraddha Pai & Carolyn Ptak & Juozas Gordevičius & Sun-Chong, 2013. "DNA unmethylome profiling by covalent capture of CpG sites," Nature Communications, Nature, vol. 4(1), pages 1-10, October.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3190
    DOI: 10.1038/ncomms3190
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms3190
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms3190?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3190. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.