Allele-specific underacetylation of histone H4 downstream from promoters is associated with X-inactivation in human cells

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.

A chromosomal memory triggered by Xist regulates histone methylation in X inactivation

We have elucidated the kinetics of histone methylation during X inactivation using an inducible Xist expression system in mouse embryonic stem (ES) cells. Previous reports showed that the ability of Xist to trigger silencing is restricted to an early window in ES cell differentiation. Here we show that this window is also important for establishing methylation patterns on the potential inactive X chromosome. By immunofluorescence and chromatin immunoprecipitation experiments we show that histone H3 lysine 27 trimethylation (H3K27m3) and H4 lysine 20 monomethylation (H4K20m1) are associated with Xist expression in undifferentiated ES cells and mark the initiation of X inactivation. Both marks depend on Xist RNA localisation but are independent of silencing. Induction of Xist expression after the initiation window leads to a markedly reduced ability to induce H3K27m3, whereas expression before the restrictive time point allows efficient H3K27m3 establishment. Our data show that Xist expression early in ES cell differentiation establishes a chromosomal memory, which is maintained in the absence of silencing. One consequence of this memory is the ability to introduce H3K27m3 efficiently after the restrictive time point on the chromosome that has expressed Xist early. Our results suggest that this silencing-independent chromosomal memory has important implications for the maintenance of X inactivation, where previously self-perpetuating heterochromatin structures were viewed as the principal form of memory.

Heterochromatin and tri-methylated lysine 20 of histone H4 in animals

Tri-methylated lysine 20 on histone H4 (Me(3)K20H4) is a marker of constitutive heterochromatin in murine interphase and metaphase cells. Heterochromatin marked by Me(3)K20H4 replicates late during S phase of the cell cycle. Serum starvation increases the number of cells that exhibit high levels of Me(3)K20H4 at constitutive heterochromatin. Me(3)K20H4 is also present at the centromeric heterochromatin of most meiotic chromosomes during spermatogenesis and at the pseudoautosomal region, as well as at some telomeres. It is not present on the XY-body. During murine embryogenesis the maternal pronucleus contains Me(3)K20H4; Me(3)K20H4 is absent from the paternal pronucleus. On Drosophila polytene chromosomes Me(3)K20H4 is present in a 'punctate pattern' at many chromosomal bands, including the chromocenter. In coccids it is present on the facultatively heterochromatinised paternal chromosome set. We also present evidence that Me(3)K20H4 is dependent upon H3-specific Suv(3)9 histone methyltransferase activity, suggesting that there may be 'epigenetic cross-talk' between histones H3 and H4.