The hidden side of unstable DNA repeats: Mutagenesis at a distance

Abstract

Structure-prone DNA repeats are common components of genomic DNA in all kingdoms of life. In humans, these repeats are linked to genomic instabilities that result in various hereditary disorders, including many cancers. It has long been known that DNA repeats are not only highly polymorphic in length but can also cause chromosomal fragility and stimulate gross chromosomal rearrangements, i.e., deletions, duplications, inversions, translocations and more complex shuffles. More recently, it has become clear that inherently unstable DNA repeats dramatically elevate mutation rates in surrounding DNA segments and that these mutations can occur up to ten kilobases away from the repetitive tract, a phenomenon we call repeat-induced mutagenesis (RIM). This review describes experimental data that led to the discovery and characterization of RIM and discusses the molecular mechanisms that could account for this phenomenon.

Keywords: Cancer; Chromosomal fragility; Contractions; DNA repeats; Expansions; Hereditary Disease; Mutagenesis; Repair; Replication; Transcription.

Fig. 1. Molecular mechanisms leading to repeat-induced mutagenesis

(A) Short repeats block transcription by forming alternative DNA structures or R-loops. This initiates ‘gratuitous’ transcription-coupled repair (TCR) and generates single strand breaks (SSBs) that can be converted to double strand breaks (DSBs). To repair the break, the ends undergo resection and single-strand annealing followed by gap-filling through TLSDNA polymerases that gives rise to mutations on either side of the repeat tract. (B) Long repeats block replication fork progression and result in reversed forks that are similar to Holliday junctions. Upon isomerization and resolution, these structures generate a one-ended DSB, which can be repaired by break-induced replication (BIR). During BIR, the end undergoes resection followed by invasion and copying of several kilobases of DNA from the donor. Due to the conservative mode of replication in BIR, DNA synthesis is highly error-prone and gives rise to mutations at large distances from the initial break site. Unrepaired SSBs generated by gratuitous TCR can also give rise to a one-ended DSB upon replication. (C) Long structure-prone repeats can form unusual DNA structures even in the G1 phase of the cell cycle. Cleavage of these structures leads to the formation of two-ended DSBs that can anneal ‘out-of-register’ and undergo homologous recombination (HR) repair. Gap-filling of the resected ends by error-prone DNA polymerases can give rise to mutations on either side and at large distances from the break site. In the case of (A) and (C), mutations will be incorporated in the next round of replication (not shown). Repetitive strands are shown in red and green. Dashed lines indicate DNA synthesized during repair and yellow star indicates mutations.