Large-Scale Heterochromatin Remodeling Facilitates Overreplicatin-Associated DNA Damage in Plant

Heterochromatin, often containing densely packaged repetitive DNA, is a challenging environment in which to repair DNA damage. In Arabidopsis interphase nuclei, pericentromeric heterochromatin is compacted into DAPI-dense chromocenters which are marked by histone modifications such as H3K27me1. Loss of H3K37me1 due to mutations in the homologous H3K27 monomethyltransferases, ATXR5 and ATXR6, lead to defects in DNA replication which results in over-production of heterochromatic DNA. Here we show that overreplication results in severe heterochromatic DNA damage and extensive chromocenter remodeling into unique sub-nuclear structures, which we named overreplication-associated centers (RACs). RACs have a highly ordered structure, with an outer layer of condensed heterochromatin, an inner layer enriched in the histone variant H2AX, and a low-density core. RACs are likely specialized compartments that are actively involved in heterochromatic DNA-damage repair, as phosphorylated H2Ax foci and DNA repair enzymes are found in the cores of RACs and that their formation is dependent upon ATM/ATR pathway. In animal cells, it has been reported that heterochromatic DNA breaks are translocated into eachromatic domain for repair. Our results show that plants may employ a variation on this strategy by undergoing a large-scale remodeling to create a compartment with low chromatin density within the heterochamtic domain to facilitate DNA damage repair.