Regulation of homologous recombination in eukaryotes

Abstract

Homologous recombination (HR) is required for accurate chromosome segregation during the first meiotic division and constitutes a key repair and tolerance pathway for complex DNA damage, including DNA double-strand breaks, interstrand crosslinks, and DNA gaps. In addition, recombination and replication are inextricably linked, as recombination recovers stalled and broken replication forks, enabling the evolution of larger genomes/replicons. Defects in recombination lead to genomic instability and elevated cancer predisposition, demonstrating a clear cellular need for recombination. However, recombination can also lead to genome rearrangements. Unrestrained recombination causes undesired endpoints (translocation, deletion, inversion) and the accumulation of toxic recombination intermediates. Evidently, HR must be carefully regulated to match specific cellular needs. Here, we review the factors and mechanistic stages of recombination that are subject to regulation and suggest that recombination achieves flexibility and robustness by proceeding through metastable, reversible intermediates.

Figure 1. Pathways of DSB repair

Protein names refer to the budding yeast S. cerevisiae (black). Where different in human, names (brown) are given in brackets. For proteins without yeast homolog brackets for human proteins are omitted. Broken lines indicate new DNA synthesis and stretches of hDNA that upon MMR can lead to gene conversion.

Figure 2. Pathways and regulation at stalled replication forks

PCNA modification regulates the choice of competing pathways for stalled replication fork recovery. A stalled fork triggers the DDR, which directly activates HR. The relationship between the DDR and cell cycle control to PCNA sumoylation/ubiquitylation has not been determined yet.

Figure 3. Homologous recombination is regulated by cell cycle control and DNA damage signaling

(a) The cell cycle controls the competition between NHEJ and HR in DSB repair. Cell cycle stages are color-coded: Red, HR is least active and green, HR is most active. Cdc28 is the sole CDK responsible for cell cycle progression in S. cerevisiae, and partners with the indicated cyclins. In mammals, six CDKs drive cell cycle progression and their relative importance varies in different tissue types. (b) The DDR results in HR activation and inhibition of cell cycle progression. The relationship between the DDR and the FANC pathway as well as PCNA sumoylation/ubiquitylation is poorly understood.

Figure 4. Model: Reversible, meta-stable intermediates in homologous recombination

HR is proposed to involve key intermediates that are reversible and meta-stable including: (1) the Rad51–ssDNA filament, (2) the initial D-loop, (3) the extended D-loop, and (4) the double Holliday junction. The dead-end complex of Rad51/Dmc1 with dsDNA, although not an HR intermediate, can be added to this list of reversible HR protein-DNA complexes (69).