A unique family of Mrr-like modification-dependent restriction endonucleases

作者：Zheng Yu^*; Cohen Karni Devora; Xu Derrick; Chin Hang Gyeong; Wilson Geoffrey; Pradhan Sriharsa; Roberts Richard J

来源：Nucleic Acids Research, 2010, 38(16): 5527-5534.

DOI：10.1093/nar/gkq327

Mrr superfamily of homologous genes in microbial genomes restricts modified DNA in vivo. However, their biochemical properties in vitro have remained obscure. Here, we report the experimental characterization of MspJI, a remote homolog of Escherichia coli's Mrr and show it is a DNA modification-dependent restriction endonuclease. Our results suggest MspJI recognizes (CNNR)-C-m (R = G/A) sites and cleaves DNA at fixed distances (N-12/N-16) away from the modified cytosine at the 3' side (or N-9/N-13 from R). Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine. Several other close homologs of MspJI show similar modification-dependent endonuclease activity and display substrate preferences different from MspJI. A unique feature of these modification-dependent enzymes is that they are able to extract small DNA fragments containing modified sites on genomic DNA, for example similar to 32 bp around symmetrically methylated CG sites and similar to 31 bp around methylated CNG sites. The digested fragments can be directly selected for high-throughput sequencing to map the location of the modification on the genomic DNA. The MspJI enzyme family, with their different recognition specificities and cleavage properties, provides a basis on which many future methods can build to decode the epigenomes of different organisms.

• 出版日期2010-9
• 单位New England Biolabs