Imaging the response to DNA damage in heterochromatin domains reveals core principles of heterochromatin maintenance

Abstract

Heterochromatin is a critical chromatin compartment, whose integrity governs genome stability and cell fate transitions. How heterochromatin features, including higher-order chromatin folding and histone modifications associated with transcriptional silencing, are maintained following a genotoxic stress challenge is unknown. Here, we establish a system for targeting UV damage to pericentric heterochromatin in mammalian cells and for tracking the heterochromatin response to UV in real time. We uncover profound heterochromatin compaction changes during repair, orchestrated by the UV damage sensor DDB2.Importantly, the restoration of heterochromatin folding is uncoupled from the maintenance of heterochromatin-specific histone modifications. We also unveil a central role for the methyltransferase SETDB1 in the maintenance of heterochromatic histone marks after UV, SETDB1 coordinating H3 methylation with new histone deposition by histone H3 chaperones in damaged heterochromatin. Our data thus shed light on fundamental molecular mechanisms safeguarding higher-order chromatin integrity following DNA damage.

Multi - level dynamics of heterochromatin and repair sites undergoing homologous recombination

“…Repair defects after HELLS RNAi can be rescued by treatment with chloroquine, which relaxes the chromatin, consistent with a role for HELLS in heterochromatin relaxation during repair [33] . In line with a role for local heterochromatin loosening to facilitate DNA repair, decompaction of mouse chromocenters has also been detected after 405nm [28] or UV [34] laser treatments, and has been linked to histone H1 displacement in response to UV damage [34] .…”

“…Super resolution imaging of heterochromatic regions and studies in response to laser-induced DSBs suggest that H3K9me3 is largely retained during chromatin relaxation at IR or Cas9induced DSBs targeting the major satellite, in mammalian cells [29,35] . Similarly, UV-induced heterochromatin relaxation occurs in conditions that maintain H3K9me3 and HP1α [34] . However, ChIP analysis identified a Kdm4A-dependent increase in H3K9me1 and H3K56me1 at site-specific heterochromatic DSBs in Drosophila [36] , and Kdm4A is required for relocalization of heterochromatic DSBs [36,37] , suggesting a local reduction of silencing during focus dynamics.…”

Histone Variants: Guardians of Genome Integrity

“…H1.2 eviction in particular spans over megabases around the break, highlighting large scale chromatin rearrangements [71]. Note that histone H1 displacement has also been observed at UVC damage sites for H1.0 and H1.4 variants [72]. Given the well established role of linker histones in chromatin compaction [8], it is tempting to speculate that H1 loss from damaged chromatin may contribute to chromatin decompaction and enhanced accessibility to repair factors.…”