In plant genomes, there exist discrete regions rich in CpG dinucleotides, namely 
CpG clusters. In rice, most of these CpG clusters are associated with genes. 
Rice genes are grouped into one of the five classes according to the position of 
an associated CpG cluster. Among them, class 1 genes, which harbor a CpG cluster 
at the 5'-terminus, share similarities with human genes having CpG islands. In 
the present study, by analyzing plant genome sequence data, primarily from rice, 
we investigated the chromosomal distribution of genes of each class, mainly 
class 1 genes. Class 1 genes were not uniformly distributed across the rice 
genome, but were clustered into discrete chromosomal segments. EST-based 
analysis of the distribution of expressed genes indicates that this segmental 
distribution of class 1 genes caused a preferential distribution of expressed 
genes within class 1 gene-rich segments. We then compared the methylation status 
of genes of each class to examine the possibility that differential DNA 
methylation, if any, is relevant to the observed differential expression level 
of genes inside and outside the class 1 segments. The difference in the 
methylation level between these genes was revealed to be fairly small, which 
does not support the above-mentioned possibility.