title: DNA unmethylome profiling by covalent capture of CpG sites.
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.
authors.affiliation: Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania.
authors.forename: Edita
authors.initials: E
authors.lastname: Kriukienė
authors.forename: Viviane
authors.initials: V
authors.lastname: Labrie
authors.forename: Tarang
authors.initials: T
authors.lastname: Khare
authors.forename: Giedrė
authors.initials: G
authors.lastname: Urbanavičiūtė
authors.forename: Audronė
authors.initials: A
authors.lastname: Lapinaitė
authors.forename: Karolis
authors.initials: K
authors.lastname: Koncevičius
authors.forename: Daofeng
authors.initials: D
authors.lastname: Li
authors.forename: Ting
authors.initials: T
authors.lastname: Wang
authors.forename: Shraddha
authors.initials: S
authors.lastname: Pai
authors.forename: Carolyn
authors.initials: C
authors.lastname: Ptak
authors.forename: Juozas
authors.initials: J
authors.lastname: Gordevičius
authors.forename: Sun-Chong
authors.initials: SC
authors.lastname: Wang
authors.forename: Artūras
authors.initials: A
authors.lastname: Petronis
authors.forename: Saulius
authors.initials: S
authors.lastname: Klimašauskas
mesh_terms: D001710:Biotin / Q000737:chemistry; D002460:Cell Line; D018899:CpG Islands; D003596:Cytosine / Q000378:metabolism; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism; D016172:DNA Fingerprinting / Q000379:methods*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D017397:Prefrontal Cortex / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D013094:Spermatozoa / Q000378:metabolism*
chemical_list: D001710:Biotin; D003596:Cytosine; D004248:DNA (Cytosine-5-)-Methyltransferases