Variation in Xi chromatin organization and correlation of the H3K27me3 chromatin territories to transcribed sequences by microarray analysis

The heterochromatin of the inactive X chromosome (Xi) is organized into nonoverlapping bands of trimethylated lysine-9 of histone H3 (H3K9me3) and trimethylated lysine-27 of histone H3 (H3K27me3). H3K27me3 chromatin of the Xi is further characterized by ubiquitylated H2A and H4 monomethylated at lysine-20. A detailed examination of the metaphase H3K9me3 pattern revealed that banding along the chromosome arms is not a consistent feature of the Xi in all cell lines, but instead is generally restricted to the centromere and telomeres. However, H3K9me3 does form a reproducible band centered at Xq13 of the active X. In contrast, H3K27me3 banding is a feature of all Xi, but the precise combination and frequency of bands is not consistent. One notable exception is a common band at Xq22-23 that spans 12-15 Mb. The detailed examination of the chromatin territory by microarray analysis refined the H3K27me3 band as well as revealed numerous less extensive clusters of H3K27me3 signals. Furthermore, the microarray analysis indicates that H3K27me3 bands are directly correlated with gene density. The reexamination of the chromosome wide banding indicates that other major H3K27me3 bands closely align with regions of highest gene density.