DNA unmethylome profiling by covalent capture of CpG sites

Edita Kriukienė, Viviane Labrie, Tarang Khare, Giedrė Urbanavičiūtė, Audronė Lapinaitė, Karolis Koncevičius, Daofeng Li, Ting Wang, Shraddha Pai, Carolyn Ptak, Juozas Gordevičius, Sun-Chong Wang, Artūras Petronis () and Saulius Klimašauskas ()
Additional contact information
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
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

Nature Communications, 2013, vol. 4, issue 1, 1-10

Abstract: 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.

Date: 2013
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DOI: 10.1038/ncomms3190

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