Dynamics and Memory of Heterochromatin in Living Cells

Abstract

Summary Posttranslational histone modifications are important for gene regulation, yet the mode of propagation and the contribution to heritable gene expression states remains controversial. To address these questions, we developed a Chromatin in vivo (CiA) Assay system employing chemically-induced proximity to initiate and terminate chromatin modifications in living cells. We selectively recruited HP1α to induce H3K9me3-dependent gene silencing and describe the kinetics and extent of chromatin modifications at the Oct4 locus in fibroblasts and pluripotent cells. H3K9me3 propagated symmetrically and continuously at rates of ~0.18 nucleosomes/hr to produce domains of up to 10kb. After removal of the HP1α stimulus, heterochromatic domains were heritably transmitted, undiminished through multiple cell generations. Our data enabled quantitative modeling of reaction kinetics, which revealed that dynamic competition between histone marking and turnover determines the boundaries and stability of H3K9me3 domains. Applying this framework, we were able to predict the steady-state dynamics and spatial features of the majority of euchromatic H3K9me3 domains.

Characterization and dynamics of pericentromere-associated domains in mice

“…However, it does not preclude a role for chromocenters in active contribution gene repression. A hint that this may occur comes from the artificial recruitment of heterochromatin protein 1 variants (HP1) to a transgene, which was previously shown to cause increased association with chromocenters (Ayyanathan et al 2003) and to induce gene silencing (Ayyanathan et al 2003;Hathaway et al 2012). However, these experiments did not allow discerning whether the two effects were causally related: Silencing could have been induced by pericentromeric recruitment, but pericentromeric association may also have been the consequence of HP1-induced gene silencing (Ayyanathan et al 2003;Hathaway et al 2012).…”

Dynamics of inherently bounded histone modification domains

“…These domains also typically show peaked patterns of enrichment, rather than broad, flat plateaus (20). We recently showed that small-molecule-mediated recruitment of HP1α to the Oct4 (Pou5f1) locus gives rise to a symmetric and peaked H3K9me3 domain in both mouse ES cells and fibroblasts (20). This domain grew continuously over time to between 2 and 10 kbp while maintaining its peaked shape, allowing us to obtain kinetic measurements on the dynamics of H3K9me3 propagation in vivo.…”

“…In mouse embryonic stem cells, the vast majority of noncentromeric H3K9me3 domains span less than 10 kbp, with most less than 5 kbp (18,19). These domains also typically show peaked patterns of enrichment, rather than broad, flat plateaus (20). We recently showed that small-molecule-mediated recruitment of HP1α to the Oct4 (Pou5f1) locus gives rise to a symmetric and peaked H3K9me3 domain in both mouse ES cells and fibroblasts (20).…”

“…Additionally, the enrichment profile and dynamics of this domain were consistent with those of H3K9me3 domains throughout the mouse genome. In our previous work, we showed that this synthetic H3K9me3 domain and >99% of all euchromatic H3K9me3 domains were well described by an "inherently bounded" model of histone modification dynamics (20), where propagation of the H3K9me3 mark was opposed by random turnover.…”

Chromatin computation: Epigenetic inheritance as a pattern reconstruction problem

“…Acetylation events are measured in the order of minutes, while methylation events are stable for days (Barth and Imhof, 2010). These rate differences are determined by the enzymes that catalyze the corresponding reactions (Hathaway et al, 2012). A given mark can be removed either by specific de-modification enzymes or through chromatin remodeling (e.g., histone turnover or histone tail clipping).…”