title: Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a.
abstract: Current evidence indicates that methylation of cytosine in mammalian DNA is restricted to both strands of the symmetrical sequence CpG, although there have been sporadic reports that sequences other than CpG may also be methylated. We have used a dual-labeling nearest neighbor technique and bisulphite genomic sequencing methods to investigate the nearest neighbors of 5-methylcytosine residues in mammalian DNA. We find that embryonic stem cells, but not somatic tissues, have significant cytosine-5 methylation at CpA and, to a lesser extent, at CpT. As the expression of the de novo methyltransferase Dnmt3a correlates well with the presence of non-CpG methylation, we asked whether Dnmt3a might be responsible for this modification. Analysis of genomic methylation in transgenic Drosophila expressing Dnmt3a reveals that Dnmt3a is predominantly a CpG methylase but also is able to induce methylation at CpA and at CpT.
authors.affiliation: Department of Hematology, Western General Hospital, EH4 2XU Edinburgh, United Kingdom. bernard.ramsahoye@ed.ac.uk
authors.forename: B H
authors.initials: BH
authors.lastname: Ramsahoye
authors.forename: D
authors.initials: D
authors.lastname: Biniszkiewicz
authors.forename: F
authors.initials: F
authors.lastname: Lyko
authors.forename: V
authors.initials: V
authors.lastname: Clark
authors.forename: A P
authors.initials: AP
authors.lastname: Bird
authors.forename: R
authors.initials: R
authors.lastname: Jaenisch
mesh_terms: D044503:5-Methylcytosine; D000818:Animals; D030801:Animals, Genetically Modified; D001483:Base Sequence; D003001:Cloning, Molecular; D003596:Cytosine / Q000031:analogs & derivatives / Q000032:analysis; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation; D000090205:DNA Methyltransferase 3A; D015226:Dinucleoside Phosphates; D004331:Drosophila melanogaster; D004622:Embryo, Mammalian; D004625:Embryo, Nonmammalian; D005314:Embryonic and Fetal Development; D008322:Mammals; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D015183:Restriction Mapping; D013234:Stem Cells / Q000201:enzymology / Q000502:physiology*
chemical_list: D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; D000090205:DNA Methyltransferase 3A; D015226:Dinucleoside Phosphates; C015772:CpG dinucleotide