Chromatin dynamics in DNA double-strand break repair

Abstract

DNA double-strand breaks (DSBs) occur in the context of a highly organized chromatin environment and are, thus, a significant threat to the epigenomic integrity of eukaryotic cells. Changes in break-proximal chromatin structure are thought to be a prerequisite for efficient DNA repair and may help protect the structural integrity of the nucleus. Unlike most bona fide DNA repair factors, chromatin influences the repair process at several levels: the existing chromatin context at the site of damage directly affects the access and kinetics of the repair machinery; DSB induced chromatin modifications influence the choice of repair factors, thereby modulating repair outcome; lastly, DNA damage can have a significant impact on chromatin beyond the site of damage. We will discuss recent findings that highlight both the complexity and importance of dynamic and tightly orchestrated chromatin reorganization to ensure efficient DSB repair and nuclear integrity. This article is part of a Special Issue entitled: Chromatin in time and space.

Figure 1. Chromatin dynamics in DSB repair

DSBs can occur in euchromatin (A, left panel) or heterochromatin (A, right panel). In both cases, phosphorylation of H2AX occurs soon after DSB induction and is followed by recruitment of MDC1 and downstream repair factors as well as histone modifiers (B). Heterochromatic lesions are not easily accessible to downstream repair factors such as the MRN complex. In yeast and flies, these lesions are, thus, protruded to the heterochromatic periphery by the SMC5/6 complex (B, right panel). Displacement of phosphorylated HP1 and KAP1 has also been reported as a means to make heterochromatic DNA lesions accessible. Removal of HP1 renders H3K9me3 accessible for Tip60 binding, which in turn acetylates histone H4 to promote chromatin relaxation. If the latter is also responsible for Tip60 recruitment in euchromatin remains to be determined. Once protruded, it is likely that repair of DSB-containing heterochromatic DNA follows the same principles as euchromatic repair (B, left panel). A large number of histone modifiers (HMs) and chromatin remodeling complexes as well as histone chaperones (e.g. ASF1) have been implicated in this process and are described in more detail in the text. Unlike heterochromatin, euchromatic chromatin is generally transcriptionally active and DSB repair is associated with pausing of RNA polymerase II (RNA PolII) in cis. (C) Recent work suggests that initial chromatin relaxation is followed by chromatin compaction, which is supported by the transient eviction of RNA PolII and the accumulation of HP1 at DSB sites. NuRD-mediated chromatin remodeling may be involved in chromatin compaction. It is unclear if compaction occurs during or after the religation of DSBs. Kinetic data support the former as numerous repair factors are retained at the DSB site for prolonged periods of time. Green arrows indicate addition of a component or modification, red arrows indicate removal.

Figure 2. Global impact of DSBs on nuclear integrity

DSBs can cause a variety of changes to chromatin structure and overall nuclear organization, all of which can have a profound impact on nuclear integrity and ultimately cell function (see text, section 4). Interestingly, the majority of these changes appear to depend on DNA damage signaling involving ATM and/or ATR kinases, suggesting global translation of a local DNA damage signal. CM, chromatin modifier.