title: The MspJI family of modification-dependent restriction endonucleases for epigenetic studies.
abstract: MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site. Here, we present the biochemical characterization of several MspJI homologs, including FspEI, LpnPI, AspBHI, RlaI, and SgrTI. All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N(12)/N(16)) away from the modified cytosine. Each displays its own sequence context preference, favoring different nucleotides flanking the modified cytosine. By cleaving on both sides of fully modified CpG sites, they allow the extraction of 32-base long fragments around the modified sites from the genomic DNA. These enzymes provide powerful tools for direct interrogation of the epigenome. For example, we show that RlaI, an enzyme that prefers (m)CWG but not (m)CpG sites, generates digestion patterns that differ between plant and mammalian genomic DNA, highlighting the difference between their epigenomic patterns. In addition, we demonstrate that deep sequencing of the digested DNA fragments generated from these enzymes provides a feasible method to map the modified sites in the genome. Altogether, the MspJI family of enzymes represent appealing tools of choice for method development in DNA epigenetic studies.
authors.affiliation: Molecular Biology, Cell Biology, and Biochemistry Program, Boston University, Boston, MA 02215, USA.
authors.forename: Devora
authors.initials: D
authors.lastname: Cohen-Karni
authors.forename: Derrick
authors.initials: D
authors.lastname: Xu
authors.forename: Lynne
authors.initials: L
authors.lastname: Apone
authors.forename: Alexey
authors.initials: A
authors.lastname: Fomenkov
authors.forename: Zhiyi
authors.initials: Z
authors.lastname: Sun
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Davis
authors.forename: Shannon R Morey
authors.initials: SR
authors.lastname: Kinney
authors.forename: Megumu
authors.initials: M
authors.lastname: Yamada-Mabuchi
authors.forename: Shuang-yong
authors.initials: SY
authors.lastname: Xu
authors.forename: Theodore
authors.initials: T
authors.lastname: Davis
authors.forename: Sriharsa
authors.initials: S
authors.lastname: Pradhan
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Roberts
authors.forename: Yu
authors.initials: Y
authors.lastname: Zheng
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D002460:Cell Line; D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D019175:DNA Methylation; D004262:DNA Restriction Enzymes / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods*; D015723:Gene Library; D005821:Genetic Techniques; D006367:HeLa Cells; D006801:Humans; D019169:Jurkat Cells; D008969:Molecular Sequence Data; D017386:Sequence Homology, Amino Acid
chemical_list: D004247:DNA; D004262:DNA Restriction Enzymes