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 analyses with the isolated AFLP fragments as probes. CpGs located in single- or low-copy-sequence regions could be grouped into two classes on the basis of their methylation status: methylation status at the class 1 CpG sites was conserved among genetically diverse rice cultivars, whereas cultivar-specific differential methylation was frequently detected among the cultivars at the class 2 CpG sites. The frequency of occurrence of methylation polymorphism between a pair of cultivars was not related to the genetic distance between the two. Through mapping, five class 2 CpG sites were localized on different chromosomes and were not clustered together in the genome. Segregation analysis of the cultivar-specific methylations with their target sites indicated that the differential methylation was stably inherited in a Mendelian fashion over 6 generations, although alterations in the methylation status at the class 2 CpG sites were observed with a low frequency.
Hokuriku National Agricultural Experiment Station, Joetsu, Niigata, Japan. ashikawa@inada.affrc.go.jp
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D002874:Chromosome Mapping; D018899:CpG Islands / Q000235:genetics*; D003596:Cytosine / Q000378:metabolism; D019175:DNA Methylation; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D013045:Species Specificity; D018911:Trinucleotide Repeats / Q000235:genetics
D018744:DNA, Plant; D003596:Cytosine