Nonmethylated transposable elements and methylated genes in a chordate genome

The genome of the invertebrate chordate Ciona intestinalis was found to be a stable mosaic of methylated and nonmethylated domains. Multiple copies of an apparently active long terminal repeat retrotransposon and a long inter spersed element are nonmethylated and a Large fraction of abundant short in terspersed elements are also methylation free. Genes, by contrast, are pred ominantly methylated. These data are incompatible with the genome defense m odel which proposes that DNA methylation in animals is primarily targeted t o endogenous transposable elements. Cytosine methylation in this urochordat e may be preferentially directed to genes.