New insights and challenges in mismatch repair: getting over the chromatin hurdle

Abstract

DNA mismatch repair (MMR) maintains genome stability primarily by repairing DNA replication-associated mispairs. Because loss of MMR function increases the mutation frequency genome-wide, defects in this pathway predispose affected individuals to cancer. The genes encoding essential eukaryotic MMR activities have been identified, as the recombinant proteins repair 'naked' heteroduplex DNA in vitro. However, the reconstituted system is inactive on nucleosome-containing heteroduplex DNA, and it is not understood how MMR occurs in vivo. Recent studies suggest that chromatin organization, nucleosome assembly/disassembly factors and histone modifications regulate MMR in eukaryotic cells, but the complexity and importance of the interaction between MMR and chromatin remodeling has only recently begun to be appreciated. This article reviews recent progress in understanding the mechanism of eukaryotic MMR in the context of chromatin structure and dynamics, considers the implications of these recent findings and discusses unresolved questions and challenges in understanding eukaryotic MMR.

Keywords: Chromatin; Genetic instability; H3K36me3; Histone modification; Mismatch repair.

Figure 1. Eukaryotic DNA mismatch repair

In eukaryotic cells, MMR is nick-directed and targeted to the newly-synthesized DNA strand. MMR begins with mismatch recognition by MutSα or MutSβ (not shown), which triggers concerted interactions/communications between MutSα, MutLα, PCNA and RPA, leading to the recruitment of EXO1 at a nearby nick. EXO1 then excises from the nick to the mismatch to generate a single-stranded DNA gap, which is filled by DNA polymerase (pol) δ in the presence of PCNA, RFC and RPA, followed by ligase I-catalyzed nick ligation. The image was reproduced from [87].

Figure 2. Recruitment of hMutSα to replicating chromatin

SETD2 converts H3K36me2 to H3K36me3, which interacts with the hMSH6 PWWP domain to localize hMutSα to chromatin before DNA replication initiates. During DNA replication, nucleosomes are disassembled and the H3K36me3-PWWP interaction is disrupted, releasing hMutSα from nucleosomes. hMutSα readily binds to nascent DNA independent of PCNA, and recognizes newly-formed mismatches to initiate MMR. This image was reproduced from Ref. [15] with permission.

Figure 3. Competing MMR models

(A) The Kolodner-Hombauer MMR model (modified from Ref. [21]. Mismatch-bound MutSα recruits multiple molecules of MutLα to heteroduplex DNA; MutLα distributes bidirectionally from the mismatch, which activates the MutLα endonuclease, recruits EXO1 to either a pre-existing or a MutLα-generated nick, and initiates DNA excision. (B) The moving and stationary models (modified from Ref. [4]). In the stationary model (right), MutS remains bound at the mismatch. Interactions between MutS, MutL and other MMR components induce DNA bending or looping, bringing the mismatch and the nick together. There are two 'moving' models: the translocation model (left) and the sliding model (middle), in which MutS binds to the mismatch and then moves away from the mismatch in a search for the strand discrimination signal (i.e., a nick). In the translocation model, MutS creates a DNA loop as it moves from the mismatch to the nick, where it recruits EXO1 to initiate DNA excision. In the sliding model (middle), ADP-bound MutS encounters the mismatch, which triggers ADP to ATP exchange and promotes bi-directional sliding away from the mismatch, so that the mismatch is available for binding by a second incoming MutS protein. Mismatch excision begins when MutS reaches a strand break.