DNA damage reduces heterogeneity and coherence of chromatin motions

Abstract

Chromatin motions depend on and may regulate genome functions, in particular the DNA damage response. In yeast, DNA double-strand breaks (DSBs) globally increase chromatin diffusion, whereas in higher eukaryotes the impact of DSBs on chromatin dynamics is more nuanced. We mapped the motions of chromatin microdomains in mammalian cells using diffractive optics and photoactivatable chromatin probes and found a high level of spatial heterogeneity. DNA damage reduces heterogeneity and imposes spatially defined shifts in motions: Distal to DNA breaks, chromatin motions are globally reduced, whereas chromatin retains higher mobility at break sites. These effects are driven by context-dependent changes in chromatin compaction. Photoactivated lattices of chromatin microdomains are ideal to quantify microscale coupling of chromatin motion. We measured correlation distances up to 2 µm in the cell nucleus, spanning chromosome territories, and speculate that this correlation distance between chromatin microdomains corresponds to the physical separation of A and B compartments identified in chromosome conformation capture experiments. After DNA damage, chromatin motions become less correlated, a phenomenon driven by phase separation at DSBs. Our data indicate tight spatial control of chromatin motions after genomic insults, which may facilitate repair at the break sites and prevent deleterious contacts of DSBs, thereby reducing the risk of genomic rearrangements.

Multi-Scale Imaging of the Dynamic Organization of Chromatin

“…Likewise, it was shown that the movements of H2B histones within ∼0.3 µm 2 chromatin microdomains were highly correlated. Interestingly, the correlation distances between these microdomains were up to 2 µm in the cell nucleus, spanning chromatin compartments and even beyond chromosomal territories [68]. Similarly, deep-PALM experiments emphasized the presence of spatiotemporal cross-correlations between chromatin structure and dynamics, extending several micrometers in space and tens of seconds in time [36].…”

“…Chromatin compaction was also closely correlated to constrained movement at different chromatin scales [35,43,68,104,108,109]. Heatmaps resulting from either single histone H2B tracking or tracking of H2B-bound chromatin domains showed a big heterogeneity in chromatin motion inside a nucleus, showing less movement within HC-rich regions than regions elsewhere in the genome [35,43,68,109].…”

“…Chromatin compaction was also closely correlated to constrained movement at different chromatin scales [35,43,68,104,108,109]. Heatmaps resulting from either single histone H2B tracking or tracking of H2B-bound chromatin domains showed a big heterogeneity in chromatin motion inside a nucleus, showing less movement within HC-rich regions than regions elsewhere in the genome [35,43,68,109]. Interestingly, despite evidence showing heterogeneity in chromatin dynamics due to compaction, a recent study has described a steady-state motion of interphase chromatin, independent of changes in chromatin compaction, cell cycle and DNA replication [66].…”

“…These two populations were interpreted as chromatin-bound and chromatin-free histones, respectively [65]. Interestingly, these two diffusion states were modeled as spatially separate domains within the nucleus, highlighting the heterogeneity of chromatin dynamics in living cells [67,68]. However, new evidence showed that individual histone H2B molecules can dynamically switch between slow and fast states, challenging the notion of spatially separated domains [63].…”

The order of sequential exposure of U2OS cells to gamma and alpha radiation influences the formation and decay dynamics of NBS1 foci

“…Changes in chromatin packing in response to DSBs and its remodelling facilitates access of the DNA repair machinery to DNA lesions [ 30 ]. Induction of DSBs leads to altered chromatin dynamics and chromatin motion that may impact the outcome of the DDR [ 31 ]. Monitoring of chromatin motion is possible using time-lapse florescence microscopy with sufficient spatial resolution [ 32 ].…”