DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin

Abstract

Dynamic changes in histone modification are critical for regulating DNA double-strand break (DSB) repair. Activation of the Tip60 acetyltransferase by DSBs requires interaction of Tip60 with histone H3 methylated on lysine 9 (H3K9me3). However, how H3K9 methylation is regulated during DSB repair is not known. Here, we demonstrate that a complex containing kap-1, HP1, and the H3K9 methyltransferase suv39h1 is rapidly loaded onto the chromatin at DSBs. Suv39h1 methylates H3K9, facilitating loading of additional kap-1/HP1/suv39h1 through binding of HP1's chromodomain to the nascent H3K9me3. This process initiates cycles of kap-1/HP1/ suv39h1 loading and H3K9 methylation that facilitate spreading of H3K9me3 and kap-1/HP1/suv39h1 complexes for tens of kilobases away from the DSB. These domains of H3K9me3 function to activate the Tip60 acetyltransferase, allowing Tip60 to acetylate both ataxia telangiectasia-mutated (ATM) kinase and histone H4. Consequently, cells lacking suv39h1 display defective activation of Tip60 and ATM, decreased DSB repair, and increased radiosensitivity. Importantly, activated ATM rapidly phosphorylates kap-1, leading to release of the repressive kap-1/HP1/suv39h1 complex from the chromatin. ATM activation therefore functions as a negative feedback loop to remove repressive suv39h1 complexes at DSBs, which may limit DSB repair. Recruitment of kap-1/HP1/suv39h1 to DSBs therefore provides a mechanism for transiently increasing the levels of H3K9me3 in open chromatin domains that lack H3K9me3 and thereby promoting efficient activation of Tip60 and ATM in these regions. Further, transient formation of repressive chromatin may be critical for stabilizing the damaged chromatin and for remodeling the chromatin to create an efficient template for the DNA repair machinery.histone methylation | homologous recombination D NA double-strand breaks (DSBs) are toxic and must be repaired to maintain genomic stability. Detection of DSBs requires recruitment of the mre11-rad50-nbs1 (MRN) complex to the DNA ends (1). MRN then recruits and activates the ataxia telangiectasia-mutated (ATM) kinase (2, 3) through a mechanism that also requires the Tip60 acetyltransferase (3). Tip60 directly acetylates and activates ATM's kinase activity (4-6) and functions, in combination with MRN, to promote ATM-dependent phosphorylation of DSB repair proteins (3), including histone H2AX. This process creates domains of phosphorylated H2AX (γH2AX) extending for hundreds of kilobases along the chromatin (7,8). Mdc1 then binds to γH2AX, providing a landing pad for other DSB repair proteins, including the RNF8/RNF168 ubiquitin ligases (1, 3, 9, 10). Tip60 also plays a critical role in regulating chromatin structure at DSBs as part of the NuA4-Tip60 complex (11). NuA4-Tip60 catalyzes histone exchange (via the p400 ATPase subunit) and acetylation of histone H4 (by Tip60) at DSBs (12-15), leading to the formation of open, flexible chromatin domains adjacent to the break (12, 13). These open chromatin structures then facilitate histone ub...

Histone chaperone Anp32e removes H2A.Z from DNA double-strand breaks and promotes nucleosome reorganization and DNA repair

“…Further, we showed H2A.Z retention at DSBs blocked the shift to open chromatin, indicating that the initial exchange of H2A.Z stabilizes chromatin immediately after DNA damage. Other repressive factors, including HP1 and NuRD (10,(40)(41)(42), are also rapidly, but transiently recruited to DSBs. Transient loading of H2A.Z and other repressors may therefore temporarily "heterochromatinize" nucleosomes at breaks, stabilizing the damaged chromatin, and allowing the cell time to process the chromatin for DNA repair (Fig.…”

PML induces compaction, TRF2 depletion and DNA damage signaling at telomeres and promotes their alternative lengthening

“…To what extent these finding apply to human cells is unclear, given the differences in telomere biology between humans and mice (Calado and Dumitriu, 2013). Furthermore, a number of findings demonstrate that induction of a condensed heterochromatic state can even promote DNA repair and/or homologous recombination (Ayrapetov et al, 2014;Geuting et al, 2013). A recent study of DDR signaling in U2OS cells is particularly informative on this issue (Burgess et al, 2014).…”

Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth

“…In Drosophila, cytological studies revealed that H3K9me-deficient mutants exhibit spontaneous DSBs in heterochromatin, and it was proposed that this damage is due to defective DNA replication (2,29,30). Mice lacking Lysine (K) Methyltransferase 1A (KMT1A) (SUV39H1) and KMT1B (SUV39H2) exhibit genome instability and high rates of lymphoma development (31,32), and both KMT1 enzymes and HP1 proteins have been implicated in DNA repair in animals (33)(34)(35)(36)(37)(38)(39)(40)(41)(42). These and other studies suggest that heterochromatin components have important roles during both DNA replication and DNA repair, but the heterochromatin-dependent mechanisms that maintain genome integrity remain poorly defined.…”