Specificity, propagation, and memory of pericentric heterochromatin

Abstract

The cell establishes heritable patterns of active and silenced chromatin via interacting factors that set, remove, and read epigenetic marks. To understand how the underlying networks operate, we have dissected transcriptional silencing in pericentric heterochromatin (PCH) of mouse fibroblasts. We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in living cells and found that stably bound complexes of the histone methyltransferase SUV39H1/2 demarcate the PCH state. From the experimental data, we developed a predictive mathematical model that explains how chromatin-bound SUV39H1/2 complexes act as nucleation sites and propagate a spatially confined PCH domain with elevated histone H3 lysine 9 trimethylation levels via chromatin dynamics. This “nucleation and looping” mechanism is particularly robust toward transient perturbations and stably maintains the PCH state. These features make it an attractive model for establishing functional epigenetic domains throughout the genome based on the localized immobilization of chromatin-modifying enzymes.

Generalized nucleation and looping model for epigenetic memory of histone modifications

“…They are implicitly reflected by the efficiency of the reverse reaction, which was assumed to occur uniformly throughout the domain and represents the activity of soluble antagonists and histone turnover. For H3K9me2/3, the simulated scenario describes the endogenous situation with low H3K9 methylation levels outside heterochromatin in fission yeast, low free concentration and activity of soluble Clr4/Suv39h, higher H3K9me3 loss rates, and weak chromatin-binding of demethylases compared with methyltransferases (16,32,35,36).…”

“…6A). Adjacent conditional nucleation sites were separated by seven nucleosomes to match the density previously estimated in mouse cells (32). Conditional nucleation sites are motivated by the experimental finding that Clr4/ Suv39h requires H3K9 methylation for stable recruitment to heterochromatin (28,32,47,48).…”

“…Adjacent conditional nucleation sites were separated by seven nucleosomes to match the density previously estimated in mouse cells (32). Conditional nucleation sites are motivated by the experimental finding that Clr4/ Suv39h requires H3K9 methylation for stable recruitment to heterochromatin (28,32,47,48). The strong methylation dependence is probably not caused by direct interaction of Clr4/Suv39h with methylated H3K9 alone but rather by the methylation-dependent presence of several other factors like Swi6/HP1, which form a nucleation complex that is required for stable and specific recruitment of the enzyme (32).…”

“…We conducted looping-driven spreading simulations with an initial modification level of 50%, which is similar to the H3K9me2/3 level for pericentric heterochromatin in mouse fibroblasts (see ref. 32 and references therein). To this end, 50% of all nucleosomes across the entire simulation array were randomly modified before the simulation was started.…”

“…Recently, models involving long-range interactions have also been proposed for H3K9 methylation. One study in mouse cells (32) linked heterochromatic H3K9 levels to the amount of methyltransferases that are stably tethered to chromatin and propagate the modification via long-range interactions. Another study on heterochromatin in fission yeast (33) showed how long-range interactions in combination with cooperativity can give rise to bistability, which means that chromatin domains delimited by site-specific boundary factors can adopt at least two discrete states with characteristic methylation levels that are stabilized over time.…”