Gene-associated CpG islands and the expression pattern of genes in rice

In an attempt to understand the role of gene-associated CpG islands in the expression of plant genes, I determined the position of CpG islands within their associated genes and the expression of the genes in rice tissues. I examined the expression patterns of 75 rice genes by Northern hybridization analysis using RNAs isolated from four rice tissues: leaf, root, callus, and panicle at flowering stage. From the results of this analysis, I classified most of the genes into one of two groups: expression in a single tissue and expression in two or more tissues. There was a marked correlation between the expression of a gene in two or more tissues and the presence of a CpG island in its 5'-end (class 1 CpG island). Among the genes expressed in a single tissue, the genes expressed in callus were distinct from those expressed in other tissues in that a large proportion contained a class 1 CpG island. These results suggest that plant CpG islands may be useful for deducing the expression pattern of uncharacterized genes.