Heterochromatin dynamics in DNA repair and aging

Abstract

The eukaryotic nucleus consists of a variety of chromatin domains each characterized by specific molecular and biophysical properties. Whereas euchromatin has an open chromatin structure with actively transcribed genes, heterochromatin is more condensed and transcriptionally inactive. Because chromatin organizes and regulates access to the genomic DNA, its composition and structure influence how the genome responds to DNA damage. Nevertheless, eukaryotic DNA is constantly exposed to endogenous and exogenous insults that can break or chemically modify DNA. One particularly dangerous type of DNA damage is a DNA double-strand break (DSB), which causes the DNA double helix to be completely severed. While DSB repair in euchromatin is well studied, the mechanisms operating in heterochromatin remained largely unknown. One heterochromatin subtype, facultative heterochromatin, is characterized by H3K27me3, H2AK118ub and Polycomb group (PcG) proteins. It plays a central role in silencing developmental genes and clusters into nuclear condensates, called Polycomb bodies. To investigate DSB repair in this chromatin environment, we established a single DSB induction system in Drosophila melanogaster. We found that DSBs arising within these Polycomb-repressed domains rapidly move outside Polycomb bodies to complete repair, and that this movement is dependent on the H3K27me3 demethylase dUtx and the end-resection protein CtIP. Although early steps of homologous recombination can occur within these compacted domains, dUtx-mediated demethylation is necessary for subsequent DSB movement and successful HR completion. We propose a model in which CtIP facilitates the recruitment of the dUtx to DSBs, enabling H3K27me3 removal and reduced chromatin compaction. This remodeling allows DSBs to move into a more accessible environment for efficient repair. As chromatin organization is important for DNA repair, we also investigated how constitutive heterochromatin changes during aging in Drosophila melanogaster. Constitutive heterochromatin represents a second major heterochromatin subtype and is characterized by H3K9me3 and binding of HP1a. This chromatin type is typically enriched at pericentromeric and sub-telomeric regions, silences repetitive sequences, such as satellite repeats and transposons, and forms one cytologically distinct, compact domain in Drosophila diploid cells. We observed cell-type specific heterochromatin changes during aging. For example, in Drosophila enterocytes, H3K9me3 and HP1a are redistributed, while gut progenitor cells remain largely unaffected. Notably, overexpression of the heterochromatin protein HP1a in enterocytes improved oxidative stress resistance and potentially extended lifespan. Together, our findings reveal that heterochromatin requires specialized DNA repair strategies and that maintaining their integrity supports stress resistance and may contribute to healthy aging.