Chromosome-wide, allele-specific analysis of the histone code on the human X chromosome.

Variation in the composition of chromatin has been proposed to generate a 'histone code' that epigenetically regulates gene expression in a variety of eukaryotic systems. As a result of the process of X chromosome inactivation, chromatinon the mammalian inactive X chromosome (Xi) is marked by several modifications, including histone hypoacetylation, trimethylation of lysine 9 on histone H3 (H3TrimK9) and substitution of core histone H2A with the histone variant MacroH2A. H3TrimK9 is a well-studied marker for heterochromatin in many organisms, but the distribution and function of MacroH2A are less clear. Cytologically, the Xi in human cells comprises alternating and largely non-overlapping approximately 10-15 Mb domains marked by MacroH2A and H3TrimK9. To examine the genomic deposition of MacroH2A, H3TrimK9 and acetylated histone H4 modifications on the Xi at higher resolution, we used chromatin immunoprecipitation in combination with a SNP-based assay to distinguish the Xi and active X (Xa) in a diploid female cell line and to determine quantitatively the relative enrichment of these histone code elements on the Xi relative to the Xa. Although we found a majority of sites were enriched for either MacroH2A or H3TrimK9 in a manner consistent with the cytological appearance of the Xi, a range of different histone code types were detected at different sites along the X. These findings suggest that the nature of the heterochromatin histone code associated with X inactivation may be more heterogeneous than previously thought and imply that gene silencing can be achieved by a variety of different epigenetic mechanisms whose genomic, evolutionary or developmental basis is now amenable to investigation.

Genomic and epigenomic approaches to the study of X chromosome inactivation.

X chromosome inactivation represents a compelling example of chromosome-wide, long-range epigenetic gene-silencing in mammals. The cis- and trans-acting factors that establish and maintain the patterns and levels of gene expression from the active and inactive X chromosomes remain incompletely understood; however, the availability of the complete genomic sequence of the human X chromosome, together with complementary approaches that explore the computational biology, epigenetic modifications and gene expression-profiling along the chromosome, suggests that the features of the X chromosome that are responsible for its unique forms of gene regulation are increasingly amenable to experimental analysis.