Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries

Eukaryotic genomes are organized into discrete structural and functional ch romatin domains. Here, we show that distinct site-specific histone H3 methy lation patterns define euchromatic and heterochromatic chromosomal domains within a 47-kilobase region of the mating-type locus in fission yeast. H3 m ethylated at lysine 9 (H3 Lys(9)), and its interacting Swi6 protein, are st rictly localized to a 20-kilobase silent heterochromatic interval. In contr ast, H3 methylated at lysine 4 (H3 LyS(4)) is specific to the surrounding e uchromatic regions. Two inverted repeats flanking the silent interval serve as boundary elements to mark the borders between heterochromatin and euchr omatin. Deletions of these boundary elements lead to spreading of H3 Lys(9) methylation and Swi6 into neighboring sequences. Furthermore, the H3 Lys(9 ) methylation and corresponding heterochromatin-associated complexes preven t H3 LyS(4) methylation in the silent domain.