title: Targeting DNA 5mCpG sites with chimeric endonucleases.
abstract: Cytosine modification of the dinucleotide CpG in the DNA regulatory region is an important epigenetic marker during early embryo development, cellular differentiation, and cancer progression. In clinical settings, such as anti-cancer drug treatment, it is desirable to develop research tools to characterize DNA sequences affected by epigenetic perturbations. Here, we describe the construction and characterization of two fusion endonucleases consisting of the (5)mCpG-binding domain of human MeCP2 (hMeCP2) and the cleavage domains of BmrI and FokI restriction endonucleases (REases). The chimeric (CH) endonucleases cleave M.HpaII (C(5)mCGG)-and M.SssI ((5)mCpG)-modified DNA. Unmodified DNA and M.MspI-modified DNA ((5)mCCGG) are poor substrates for the CH-endonucleases. Sequencing cleavage products of modified lambda DNA indicates that cleavage takes place outside the (5)mCpG recognition sequence, predominantly 4-17 bp upstream of the modified base (/N(4-17)(5)mCpG, where / indicates the cleavage site). Such (5)mCpG-specific endonucleases will be useful to study CpG island modification of the regulatory regions of tumor suppressor genes, and for the construction of cell-specific and tumor-specific modified CpG island databases.
authors.affiliation: New England Biolabs, Inc., 240 County Road. Ipswich, MA 01938-2723, USA.
authors.forename: Alexey
authors.initials: A
authors.lastname: Fomenkov
authors.forename: Priscilla Hiu-Mei
authors.initials: PH
authors.lastname: Too
authors.forename: Siu-Hong
authors.initials: SH
authors.lastname: Chan
authors.forename: Romas
authors.initials: R
authors.lastname: Vaisvila
authors.forename: Beth Ann
authors.initials: BA
authors.lastname: Cantin
authors.forename: Laurie
authors.initials: L
authors.lastname: Mazzola
authors.forename: Vernissia
authors.initials: V
authors.lastname: Tam
authors.forename: Shuang-yong
authors.initials: SY
authors.lastname: Xu
mesh_terms: D001483:Base Sequence; D018899:CpG Islands; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation; D004720:Endonucleases / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D006801:Humans; D008969:Molecular Sequence Data; D010957:Plasmids / Q000235:genetics; D017434:Protein Structure, Tertiary; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D013379:Substrate Specificity
chemical_list: D011993:Recombinant Fusion Proteins; D004247:DNA; D004720:Endonucleases