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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.

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