A Chromosomal Memory Triggered by Xist Regulates Histone Methylation in X Inactivation

Abstract

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.

Histone H4 lysine 20 monomethylation promotes transcriptional repression by L3MBTL1

“…Initial reports highlighted the importance of H4K20me1 in 'facultative' heterochromatin and Xinactivation (Fang et al, 2002;Nishioka et al, 2002;Kohlmaier et al, 2004;Karachentsev et al, 2005;Martens et al, 2005;Sims et al, 2006). Recently, this exclusivity has been questioned by studies that suggest a role in transcriptional competence and elongation (Talasz et al, 2005;Vakoc et al, 2006;Barski et al, 2007;Pesavento et al, 2008).…”

“…Furthermore, the methylation status (mono-, di-or tri-(me1/me2/ me3)) of specific lysines, extends the options for signaling to chromatin (Peters et al, 2003;Rice et al, 2003) as exemplified for H4K20 methylation. H4K20me1 is associated with facultative heterochromatin (Fang et al, 2002;Martens et al, 2005;Sims et al, 2006), and the inactive X chromosome (Kohlmaier et al, 2004). In contrast, H4K20me3 marks constitutive heterochromatin (Schotta et al, 2004;Mikkelsen et al, 2007).…”

Specific patterns of histone marks accompany X chromosome inactivation in a marsupial

“…First, histone modifications associated with transcriptional activity (H3K4me2, H3K9ac) are lost (Heard et al 2001;Chaumeil et al 2002;Okamoto et al 2004). Soon after, the inactive X gains specific repressive m a r k s , H 3 K 9 m e 2 / H 3 K 2 7 m e 3 / H 4 K 2 0 m e 1 / H2AK119ub (Heard et al 2001;Mermoud et al 2002;Plath et al 2003;Silva et al 2003;Rougeulle et al 2004;Kohlmaier et al 2004;de Napoles et al 2004;Fang et al 2004;Hernandez-Munoz et al 2005). Finally, it loses acetylation of histone H4 (H4Kac), which is associ-ated with active chromatin (Keohane et al 1996;Heard et al 2001;Chaumeil et al 2002;).…”

“…Finally, it loses acetylation of histone H4 (H4Kac), which is associ-ated with active chromatin (Keohane et al 1996;Heard et al 2001;Chaumeil et al 2002;). The role of histone modifications in the inactivation process is not yet understood, but it may confer the stabilization that underpins the somatic heritability of the inactive state (Kohlmaier et al 2004). Finally, other changes appear, including a shift to late replication timing (Keohane et al 1996;Chaumeil et al 2002;Okamoto et al 2004), recruitment of the histone variant macroH2A (Costanzi and Pehrson 1998;Mermoud et al 1999), and CpG island methylation of DNA (Lock et al 1987;Norris et al 1991;Sado et al 2004).…”

Incomplete penetrance and variable expressivity: is there a microRNA connection?

“…On the other hand, the molecular basis of differential expression of homologous alleles has been extensively investigated in the context of genomic imprinting and random inactivation of X chromosome in female mammals. (12)(13)(14)(15) …”