Tunable, division-independent control of gene activation timing by a polycomb switch

Abstract

SUMMARY During development, progenitors often differentiate many cell generations after receiving signals. These delays must be robust yet tunable for precise population size control. Polycomb repressive mechanisms, involving histone H3 lysine-27 trimethylation (H3K27me3), restrain the expression of lineage-specifying genes in progenitors and may delay their activation and ensuing differentiation. Here, we elucidate an epigenetic switch controlling the T cell commitment gene Bcl11b that holds its locus in a heritable inactive state for multiple cell generations before activation. Integrating experiments and modeling, we identify a mechanism where H3K27me3 levels at Bcl11b , regulated by methyltransferase and demethylase activities, set the time delay at which the locus switches from a compacted, silent state to an extended, active state. This activation delay robustly spans many cell generations, is tunable by chromatin modifiers and transcription factors, and is independent of cell division. With their regulatory flexibility, such timed epigenetic switches may broadly control timing in development.

Scalable control of developmental timetables by epigenetic switching networks

“…The time evolution of these variables is given by the following rules:Pitrue⟶αi(x1,…,xN)⋅V⋅(PT−Pi)Pi+1,Pitrue⟶βi(x1,…,xN)⋅V⋅PiPi−1,Xitrue⟶γi(x1,…,xN)⋅V⋅PiXi+1-8pcand1em1em Xitrue⟶δixi⋅VXi−1.Here, gene i switches from an inactive (active) to an active (inactive) epigenetic state with first-order kinetics, with a stochastic time constant of α i ( β i ). Consistent with work from our laboratory and others [30,38], both locus activation and silencing rates depend on x 1 … x N , such that constants for epigenetic switching depend on regulatory input levels, which may either involve transcription factors or chromatin-modifying enzymes [38]. Once in an...…”

“…Chromatin modifying enzymes, with their broad action and ability to modulate epigenetic switching at multiple gene loci, could globally alter the overall dynamics of epigenetic switching networks, and affect the speed at which temporal schedules set by these networks unfold. Consistently, disruption of chromatin modifying enzymes often results in changes to the speed of developmental transitions [38,71–73].

Figure 6Chromatin regulators can scalably expand or contract developmental timetables to modify total organ size.

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“…In accordance with our recent findings [37], we describe chromatin states at gene loci using a two-state model with heritable inactive and active states; however, we note that there could be additional hidden states that do not show observable differences in gene expression [30,45]. These epigenetic states are commonly thought to be stabilized by self-reinforcing histone modifications that create a positive feedback loop [39,40,46]; however, our recent study suggests that they may instead be stabilized by inter-nucleosomal interactions that result in the formation of a stable compacted chromatin structure [38]. Of note, this model can alone explain why histone modifications often correlate weakly with the gene activation state, and how rates of epigenetic switching can be tunably controlled by both transcription factors and chromatin regulators, in accordance with direct observations of stochastic epigenetic switching dynamics at the single-cell level [30,38].…”

“…These epigenetic states are commonly thought to be stabilized by self-reinforcing histone modifications that create a positive feedback loop [39,40,46]; however, our recent study suggests that they may instead be stabilized by inter-nucleosomal interactions that result in the formation of a stable compacted chromatin structure [38]. Of note, this model can alone explain why histone modifications often correlate weakly with the gene activation state, and how rates of epigenetic switching can be tunably controlled by both transcription factors and chromatin regulators, in accordance with direct observations of stochastic epigenetic switching dynamics at the single-cell level [30,38]. Finally, we model growth and division of individual cells, together with its interplay with gene regulatory network activity.…”

In search of lost time: Enhancers as modulators of timing in lymphocyte development and differentiation

“…Indeed, the Bcl11b locus undergoes dramatic changes in chromatin state and conformation during activation, including changes in nuclear positioning, DNA methylation, histone modifications, and long-range chromatin looping interactions. [59][60][61] To determine whether these epigenetic mechanisms contribute to timing of Bcl11b activation, the locus was studied using the dualcolor biallelic reporter approach described above ( Figure 4A). By separately tracking expression of each Bcl11b allele in single cells using live imaging, it was revealed that each allele turns on independently during T-cell development, with one allele frequently activating multiple days and cell divisions before another.…”