Synthetic epigenetic circuits to investigate robustness and adaptability of epigenetic inheritance in schizosaccharomyces pombe
Embargo Date
2026-05-22
OA Version
Citation
Abstract
Chromatin-based epigenetic regulation globally governs cell expression states in eukaryotes, credited with robustly protecting cell-specific programming in development of multicellular organisms, but also involved in developmental disorders, cancer propagation, and adaptation. This potency inspires targeting or repurposing epigenetic elements for development of next generation cellular and molecular therapies. However, defining sufficiency for integral properties such as durable inheritance has remained elusive. What are the requirements for generating robust epigenetic inheritance? Functional motifs such as “read-write” positive feedback are common in chromatin systems, and their importance in epigenetic memory in natural systems is well documented. Using bottom-up approaches, minimal synthetic epigenetic systems with “read-write” have been shown to actively propagate chromatin states, but cannot overcome antagonistic forces. Epigenetic crosstalk, another common feature in natural systems, represents a plausible mechanism for reinforcing “read-write” propagation and conferring stable epigenetic inheritance. Here, we built synthetic crosstalk between distinct kinds of modifications (histone modifications and DNA modifications) in the fission yeast Schizosaccharomyces pombe. We established a non-native DNA modification, N6-methyladenine (m6A) and characterized a set of “writer” domains. We then coupled m6A to the native heterochromatic modification H3K9me using combinations of respective “read” and “write” domains, discovering engineering limitations in pombe heterochromatin systems. We constructed complete feedback circuits that rely on artificially introduced epigenetic crosstalk between the native H3K9me and the non-native m6A. We built and screened combinations of components to uncover properties that enable crosstalk-mediated inheritance. We discover key design choices such as cooperative binding, we find engineering limits on components compatible with native machinery, and ultimately discover regimes that enable epigenetic super-memory in cells for more than 50 generations, requiring strong crosstalk and high modification site frequency. Finally, we explore how crosstalk-mediated epigenetic memory manages against perturbations to the system.
In a second project, we considered how cells make adaptive epigenetic choices. Recent studies show heterochromatin-defining H3K9me can be redistributed to establish adaptive phenotypes. We developed a precision-engineered genetic approach to trigger heterochromatin misregulation on-demand in pombe. This enabled us to trace genome-scale RNA and H3K9me changes over time in long-term, continuous cultures. Adaptive H3K9me establishes over remarkably slow timescales relative to the initiating stress but ultimately leads to cells converging on an optimal adaptive solution. Upon stress removal, cells relax to new transcriptional and chromatin states, establishing memory primed for future adaptive epigenetic responses. Collectively, we identify the slow kinetics of epigenetic adaptation that allow cells to discover and heritably encode novel adaptive solutions, with implications for drug resistance and response to infection.
Description
2025
License
Attribution 4.0 International