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

Abstract

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.

X inactivation Xplained

“…Chromosome-wide chromatin analysis of X-linked epigenetic modifications confirmed many cytological observations, including hypoacetylation of histone H4, accumulation of histone H3, K9, and K27 tri-methylation and accumulation of histone variant macroH2A on the Xi [43,44] (Figure 3b). These results suggest that a wide variety of chromatin modifiers including Polycomb group complexes, histone deacetylases, and DNA methylases act in concert to maintain repression of the Xi [45].…”

Dosage compensation and gene expression on the mammalian X chromosome: one plus one does not always equal two

“…These many epigenetic layers create redundancy to ensure that global reactivation of the X does not occur (Csankovszki et al 2001). With this in mind, it is particularly intriguing that at least some modifications do not homogenously cover the inactive X, but are spatially separated (Duthie et al 1999; Chadwick and Willard 2004; Valley et al 2006), indicating that the inactive X is clearly not just a single, uniform block of heterochromatin.…”

“…A complication for such X studies is that the two transcriptionally-distinct Xs in females each carry their own compilation of epigenetically-encoded regulatory instructions. Approaches that distinguish the active X from the inactive X are optimal (Brinkman et al 2006; Valley et al 2006; Chadwick 2007; Marks et al 2009). Such studies continue to reveal the heterogeneous nature of inactive X heterochromatin as the distribution of marks specific to gene bodies, promoters, and non-coding sequences is probed.…”

The functional role of the CARM1-SNF5 complex and its associated HMT activity in transcriptional activation by thyroid hormone receptor

“…The down regulation of mK9-H3 was abolished by treatment with siCARM1 or siSNF5. Interestingly, knockingdown either CARM1 or SNF5 inhibited the downregulation of histone macroH2A, which is correlated with transcriptional activation (Valley et al, 2006). Finally, these data indicate that the functional importance of the CARM1-SNF5 complex in histone code dynamics is correlated with transcriptional activation.…”