Abstract
Efficient repair of DNA double-strand breaks (DSBs) requires a coordinated DNA Damage Response (DDR), which includes phosphorylation of histone H2Ax, forming γH2Ax. This histone modification spreads beyond the DSB into neighboring chromatin, generating a DDR platform that protects against end disassociation and degradation, minimizing chromosomal rearrangements. However, mechanisms that determine the breadth and intensity of γH2Ax domains remain unclear. Here, we show that chromosomal contacts of a DSB site are the primary determinants for γH2Ax landscapes. DSBs that disrupt a topological border permit extension of γH2Ax domains into both adjacent compartments. In contrast, DSBs near a border produce highly asymmetric DDR platforms, with γH2Ax nearly absent from one broken end. Collectively, our findings lend insights into a basic DNA repair mechanism and how the precise location of a DSB may influence genome integrity.
Highlights
Efficient repair of DNA double-strand breaks (DSBs) requires a coordinated DNA Damage Response (DDR), which includes phosphorylation of histone H2Ax, forming γH2Ax
To probe genomic features that limit γH2Ax propagation, we characterized DDR platforms in precursor lymphocytes resulting from physiological DSBs, which are mediated by the RAG endonuclease complex during V(D)J recombination
ΓH2Ax profiles correlated with the magnitude of chromosomal contacts measured by 4C from the viewpoint of the small Jk cluster, which always harbor a DSB in the vabl system (R = 0.60, Pearson’s correlation)
Summary
Efficient repair of DNA double-strand breaks (DSBs) requires a coordinated DNA Damage Response (DDR), which includes phosphorylation of histone H2Ax, forming γH2Ax. Formation of γH2Ax serves as a checkpoint for the homologous recombination (HR) and nonhomologous end joining (NHEJ) repair pathways, through mechanisms that indirectly or directly retain effector proteins[6,7]. These effectors include 53BP1, which prevents end degradation and disassociation[8,9,10]. The mechanisms that sculpt γH2Ax domains have important implications, especially given the critical role of these platforms in damage responses, including: (1) tethering broken chromosomes until they are repaired[11,19] (2) repression of transcription[20,21], and (3) sequestration of DDR factors around a DSB site[18,22]. DSBs adjacent to TAD borders generate asymmetric γH2Ax domains, which may influence repair efficiencies and could explain the enrichment of structural variants near topological boundaries
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