DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling

Abstract

DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.

Keywords: DNA end resection; DNA repair; cell cycle; double strand break; genome stability; nucleosome remodeling.

FIGURE 1

Eukaryotic DNA end resection in the chromatin context. DNA end resection is a two step process that can be divided into short-range resection (orange) and long-range resection (yellow). Mre11-C initiates short-range resection by nicking the 5′ terminated strand in proximity to the DSB via its endonuclease activity. Then, Mre11-C generates a short 3′ ssDNA overhang close to the DSB using its 3′-5′ exonuclease function. Exo1 and STR-Dna2 carry out long-range resection and extend the length of the resected ssDNA tract through chromatin.

FIGURE 2

Nucleosome remodeler activities and their effects on chromatin. The activity of different nucleosome remodelers (shades of green) can result in three principal effects on nucleosomes. (A)–Nucleosome sliding and eviction. While all remodelers have the propensity to slide nucleosomes, eviction of nucleosomes from double-stranded DNA is catalyzed mainly by the SWI/SNF sub-family of nucleosome remodelers. (B)–Nucleosome positioning. Some nucleosome remodelers have the ability to slide and position nuclesomes on DNA in a controlled fashion that leads to the formation of regularly spaced arrays. In the budding yeast system this activity is catalyzed mainly by ISW1a-, ISW1b-, Chd1 and INO80-complexes. (C)–Nucleosome editing. Nucleosome editing is defined as the exchange of canonical histones (grey) for non-canonical histone variants, like H2A.Z (purple), within the nucleosome and vice versa. In budding yeast H2A/H2A.Z exchange is performed by the INO80 sub-family of remodelers: the SWR1-complex catalyzes the incorporation of H2A.Z-H2B dimers, while the INO80-C is thought to catalyze the reverse reaction.

FIGURE 3

Nucleosome eviction at DSBs. (A)–Resection nucleases (Exo1/Dna2) are inhibited by the presence of nucleosomes. Thus, eviction of nucleosomes from dsDNA is required to facilitate resection. This reaction may be catalyzed by nucleosome remodelers with evicting activity (light green). Moreover, binding of the Mre11-C to the DSB ends might be inhibited by nucleosomes (not shown). Therefore, eviction by nucleosome remodelers might be additionally required also for resection initiation. (B)–Incorporation of H2A.Z (purple) into nucleosomes by nucleosome remodelers with editing activity (dark green) leads to a reduced stability of nucleosomes. H2A.Z-containing nucleosomes may therefore be directly evicted by long-range resection nucleases, but nucleosome remodelers with evicting activity (light green) may be additionally involved (see “?”).

FIGURE 4

Potential mechanisms by which Fun30 may promote resection. Long-range resection is controlled by the antagonism between the resection-promoting nucleosome remodeler Fun30 and the resection-inhibiting nucleosome binder Rad9. The precise mechanism of this antagonistic relationship is still elusive, but the following models are possible: (A)–Fun30 directly removes Rad9 from nucleosomes thereby removing the factor inhibiting resection. (B)–Fun30 counteracts Rad9 association with nucleosomes by exchanging histone dimers. It either incorporates histones lacking modifications necessary for Rad9 association – for example unmodified H2A, missing phosphorylation on S129 (γH2A), or the histone variant H2A.Z; both of which eliminate Rad9 binding sites. (C)–Fun30 slides and/or evicts Rad9-bound nucleosomes, freeing the DNA from the resection-inhibitory effects of Rad9 to allow the subsequent resection.