Abstract
Chromatin regulation enables cells to establish and remember gene expression states. However, how chromatin regulators control gene expression in single cells, quantitatively and over time, has remained unclear. Using time-lapse microscopy, we addressed this question for four biochemically diverse chromatin regulators (DNMT3B, HDAC4, EED, KRAB). For all four factors, silencing and reactivation occurred in all-or-none events, allowing these regulators to modulate the fraction of silenced cells over time, rather than the level of gene expression. These dynamics could be described by a simple 3-state model involving stochastic transitions between active, reversibly silent, and irreversibly silent states. The specific transition rates of each regulator produce distinct timescales of silencing (hours to days), and types of epigenetic memory (transient—HDAC4, permanent—DNMT3B, and a hybrid of the two—EED and KRAB). These results provide a framework for understanding and engineering mammalian chromatin regulation.
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