A recent study published in Nature delves into the mechanisms behind the formation of compartments in chromatin in response to double-stranded breaks (DSBs) in DNA, and how this process orchestrates the DNA damage response (DDR).
DSBs are dangerous lesions in DNA that can lead to chromosomal rearrangements and disrupt cellular homeostasis and genetic integrity. While the role of chromatin in DNA repair has been extensively studied, the influence of chromosomal architecture on these processes is still largely unknown.
The study employed techniques such as chromatin immunoprecipitation followed by sequencing (ChIP-seq), direct DSB mapping, and Hi-C data analysis to investigate the three-dimensional (3D) genome structure and the role of specific proteins involved in the DDR, such as ataxia-telangiectasia-mutated (ATM) and DNA-dependent protein kinase (DNA-PK).
By inducing DSBs in cells, the researchers observed the formation of a novel chromatin compartment, referred to as the D compartment, composed of damaged topologically associating domains (TADs) marked with H2AX and 53BP1. This clustering of injured TADs occurred via a process called polymer-polymer phase separation (PPPS) rather than liquid-liquid phase separation (LLPs).
The D compartment, formed during the G1 phase of the cell cycle, was unaffected by cohesion and promoted by DNA-PK suppression and the accumulation of R-loops. This compartment facilitated the activation of DDR genes enriched by R-loops and provided a purpose for DSB clustering in DDR. However, DSB-induced chromosomal rearrangement also increased the risk of translocations, a phenomenon commonly observed in tumor genomes.
ATM and DNA-PK played crucial roles in activating DDR through the formation of gH2AX chromatin domains and signaling events like DDR focus formation and 53BP1 recruitment. Inhibiting ATM activity reduced DSB clustering, while inhibiting DNA-PK activity significantly enhanced clustering.
The study also found that the Linkers of the Nucleoskeleton to the Cytoskeleton (LINC) complex, the actin network, and the phase-segregation features of 53BP1 influenced DSB clustering. The selective benefit of DSB clustering or repair focal fusion is still unknown, as juxtaposing DSBs may lead to translocations.
R-loop accumulation upon DSB induction served as a hallmark of increased DDR gene targeting to the D compartment. While the rupture of compartments limited the activation of some DDR genes, increased D-compartment development caused hyperactivation of DDR genes. Relocating DDR-upregulated genes within the D compartment could explain some translocations found in cancer genomes.
In conclusion, this study sheds light on the importance of chromosomal architecture in DNA repair, specifically in the context of DSBs and DDR. ATM plays a crucial role in repairing damaged TADs, which cluster within the nucleus. DSB clustering is controlled by ATM and cell cycle regulation. The D compartment allows for the recruitment and activation of DDR-related genes but also poses a risk of translocations due to the coalescence of TADs and loop extrusion, which brings distant DSBs into close contact.
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