Chromatin remodeling at DNA double-strand breaks

Abstract

DNA double-strand breaks (DSBs) can arise from multiple sources, including exposure to ionizing radiation. The repair of DSBs involves both posttranslational modification of nucleosomes and concentration of DNA-repair proteins at the site of damage. Consequently, nucleosome packing and chromatin architecture surrounding the DSB may limit the ability of the DNA-damage response to access and repair the break. Here, we review early chromatin-based events that promote the formation of open, relaxed chromatin structures at DSBs and that allow the DNA-repair machinery to access the spatially confined region surrounding the DSB, thereby facilitating mammalian DSB repair.

Figure 1. The mechanism of double strand break repair

(Top) ATM phosphorylates H2AX at double strand breaks (−DSBs), creating a binding site for the mdc1 protein. ATM-MRN (mre11-rad50-nbs1) complexes then associate with mdc1, promoting the spreading of γH2AX along the chromatin for hundreds of kilobases. (Bottom) mdc1 recruits multiple DSB repair proteins to sites of damage, including the RNF8/RNF168 ubiquitin ligases. Chromatin ubiquitination (Ub) then facilitates loading of the brca1 complex and 53BP1 DSB repair proteins. Abbreviation: P, phosphorylation.

Figure 2. H2A.Z exchange drives H4 acetylation

Exchange of H2A for H2A.Z alters interaction between the N-terminal tail of histone H4, exposing it to acetylation by Tip60. The combination of H2A.Z exchange and H4 acetylation (Ac) functions to shift chromatin into the open, relaxed conformation required for DSB repair.

Figure 3. H2A.Z exchange drives chromatin changes that direct chromatin modification at DSBs

At double strand breaks, H2A.Z exchange promotes H4 acetylation (Ac) by Tip60, which in turn directs ubiquitination (Ub) of the chromatin by the RNF8/RNF168 ubiquitin ligases and exposure and/or methylation (Me) of H4K20me2 by MMSET. Association of NuA4-Tip60 with mdc1 is omitted for clarity. Abbreviation: P, phosphorylation.

Figure 4. Creating access to Double strand Breaks

Chronological sequence of steps in remodeling of a double strand break (DSB). Initial polyADP-ribosylation (PARylation) by PARP1 leads to rapid recruitment of NuRD and ALC1 (through interaction with PAR) and Kap-1/HP1 complexes (possibly through interaction with PAR). Deacetylation (by NurD) and proposed H3K9 methylation by lysine methyltransferases (KMTs), including suv39h1 and G9a, creates a temporary repressive chromatin structure. Subsequent phosphorylation (P) of γH2AX recruits NuA4-Tip60, promoting the ordered remodeling of the chromatin through H2A.Z exchange, histone acetylation (Ac) and chromatin ubiquitination (Ub). This creates a common chromatin template for DSB repair by either nonhomologous end joining (NHEJ) -or homologous recombination (HR)-mediated repair._ KMT, lysine methyltransferases.