Stochastic modelling reveals that chromatin folding buffers epigenetic landscapes against sirtuin depletion during DNA damage

TL;DR

This study uses stochastic modeling to show that chromatin folding helps maintain epigenetic stability during DNA damage by buffering against enzyme depletion, especially in regions with extensive long-range contacts.

Contribution

It introduces a combined stochastic and structural model revealing how chromatin architecture buffers epigenetic landscapes against sirtuin depletion during DNA damage.

Findings

Chromatin regions with long-range contacts are more resilient to epigenetic destabilization.

Sirtuin relocalization leads to epigenetic erosion, influenced by chromatin geometry.

Chromatin folding acts as a structural buffer maintaining epigenetic integrity.

Abstract

Epigenetic landscapes, represented by patterns of chemical modifications on histone tails, are essential for maintaining cell identity and tissue homeostasis. These landscapes are shaped by multiple factors, including local biochemical signals and the three-dimensional organisation of chromatin. However, their response to genomic stress, such as DNA double-strand breaks (DSBs), remains incompletely understood. Here, we use a stochastic model of histone modification dynamics integrated with chromatin architecture to investigate how local depletion of sirtuins, histone deacetylases involved in DSB repair, destabilises epigenetic patterns. Our simulations recapitulate experimental findings in which sirtuin relocalisation to DSB sites leads to the epigenetic erosion and suggest that the resulting landscape depends on enzyme levels and chromatin geometry. Importantly, chromatin regions with large domains of long-range contacts are more resilient to epigenetic destabilisation. These findings suggest that chromatin folding can buffer against relocation of histone-modifying enzymes, highlighting a structural mechanism for preserving epigenetic integrity under stress.