Surveying CpG methylation at 5 '-CCGG in the genomes of rice cultivars

We investigated the CpG methylation status of the sequence CCGG in the rice genome by using methylation-sensitive AFLP and subsequent Southern analyse s with the isolated AFLP fragments as probes. CpGs located in single- or lo w-copy-sequence regions could be grouped into two classes on the basis of t heir methylation status: methylation status at the class 1 CpG sites was co nserved among genetically diverse rice cultivars, whereas cultivar-specific differential methylation was frequently detected among the cultivars at th e class 2 CpG sites. The frequency of occurrence of methylation polymorphis m between a pair of cultivars was not related to the genetic distance betwe en the two. Through mapping, five class 2 CpG sites were localized on diffe rent chromosomes and were not clustered together in the genome. Segregation analysis of the cultivar-specific methylations with their target sites ind icated that the differential methylation was stably inherited in a Mendelia n fashion over 6 generations, although alterations in the methylation statu s at the class 2 CpG sites were observed with a low frequency.