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

Abstract

This article is part of a series of reviews covering Genome Regulation in Innate and Adaptive Immune Cells appearing in Volume 300 of Immunological Reviews.

A timed epigenetic switch balances T and ILC lineage proportions in the thymus

“…From work in diverse developmental and differentiation systems, it is now established that some cis -acting regulatory elements specifically enhance the probability a single gene stochastically switches on in response to signals, without affecting its final expression magnitude once active. As switching probabilities are low, they can frequently give rise to extended gene activation delays that span multiple cell generations, and thus can be referred to as “timing enhancers” (Chu et al, 2021). Mutations at these timing enhancers could provide a unique tool to investigate roles for gene activation timing (Nguyen et al, 2021), as they frequently result in moderate changes in the timing delays for gene activation and developmental events (Gérard et al, 1997; Zákány et al, 1997).…”

“…However, across a range of systems, epigenetic switches, acting in cis at individual gene loci, can delay the activation of lineage-specifying genes after initial exposure to developmental signals (Abadie et al, 2023; Berry et al, 2017; Bintu et al, 2016; Hathaway et al, 2012; Ng et al, 2018), sometimes by multiple days and cell generations. These time delays in epigenetic switching vary both between single cells and between individual gene loci in the same cell due to the stochastic nature of chromatin regulation (Bintu et al, 2016; Dodd et al, 2007; Festenstein et al, 1996; Owen et al, 2023) However, despite this stochasticity, probabilistic time constants of switching are precisely modulated at multiple levels, including by cytokine signaling, transcription factors (TFs), and associated cis -regulatory elements and chromatin-modifying enzymes (Chu et al, 2021; Deschamps and Duboule, 2017; Fabre et al, 2015; Kissiov et al, 2022; Pease et al, 2021). Because of their tunable nature, such timed epigenetic switches could be utilized by stem cells to control differentiation output.…”

“…By analyzing Bcl11b activation dynamics at the single chromosomal allele / single cell level, we found that this multi-day delay was due to an timed epigenetic switch, involving a rate-limiting transition of the gene locus from a compacted, silent state to a de-compacted, expressing state (Ng et al, 2018;Pease et al, 2021). Importantly, while this switch is stochastic, time constants for probabilistic switching are tightly controlled by the histone-modifying enzymes [Polycomb Repressive Complex (PRC)2] (Pease et al, 2021), upstream transcription factors (TCF-1, Gata3) (Kueh et al, 2016), as well as a far-distal cis-regulatory element (Li et al, 2013;Ng et al, 2018), which we termed a 'timing enhancer' as it moderately speeds up the onset of Bcl11b activation in progenitors but is not required for maintaining its expression (Chu et al, 2021). Time-delayed control of Bcl11b epigenetic switching and activation may play a role in T cell and ILC2 lineage decision making in early progenitors.…”

Antigen perception in T cells by long-term Erk and NFAT signaling dynamics

“…This observation suggests that when both Erk and NFAT are present, they may act together in a way that prevents one another from acting alone. In other systems ( 68 , 69 ), TFs can be redirected from one set of binding sites to another by a trans-acting binding partner, raising the possibility that AP-1 and NFAT could redirect each other from sites involving other partners to those where they bind together. To evaluate the plausibility of such a mechanism, we analyzed a series of mathematical models relating NFAT and AP-1 levels in the nucleus at steady-state to their binding to cis -regulatory elements at target gene loci and the resultant rates of transcription ( SI Appendix , Mathematical Appendix, section 1 ).…”

“…5 B –”Late”). However, because some cis -regulatory elements can control activation timing without affecting maintenance of gene expression ( 69 , 77 – 79 ), as observed for Il2ra ( 77 ), we also perturbed signaling at the onset of stimulation ( Fig. 5 B –”Early”), as Erk and NFAT may play distinct roles in controlling activation vs. maintenance of gene expression.…”