A tale of tails: insights into the coordination of 3′ end processing during homologous recombination

Abstract

SummaryEukaryotic genomes harbor a large number of homologous repeat sequences that are capable of recombining at high frequency. Their potential to disrupt genome stability highlights the need to understand how homologous recombination processes are coordinated. The S. cerevisiae Rad1-Rad10 endonuclease performs an essential role in recombination between repeated sequences by processing 3′ single-stranded intermediates formed during single-strand annealing and gene conversion events. Several recent studies have focused on factors involved in Rad1-Rad10-dependent removal of 3′ nonhomologous tails during homologous recombination, including Msh2-Msh3, Slx4, and the newly identified Saw1 protein (1-4). In addition, these studies suggest mechanisms for how DNA repair is coordinated by the DNA damage checkpoint machinery (1). This review aims to integrate these new findings with previous work to create a comprehensive model for how DNA repair and checkpoint factors act in concert to process 3′ nonhomologous tail intermediates that arise during homologous recombination. KeywordsRad1-Rad10; Saw1; Slx4; Msh2-Msh3; nonhomologous tail Homologous stretches of DNA sequences scattered throughout the genome are a threat to genome stability because of their potential to recombine. It is estimated that nearly half of the human genome consists of repetitive DNA (5,6), and genome rearrangements caused by recombination between repeats are known to contribute to a variety of human diseases, including many cancers (7)(8)(9). Repetitive sequences such as Alu elements are particularly susceptible to non-conservative homologous recombination via single-strand annealing (SSA), which results in the deletion of sequences located between the repeats (10-12). The abundance of such sequences in the human genome underscores the need for a comprehensive understanding of the homologous recombination processes that act on them.SSA is a major recombination pathway for repairing spontaneous and induced double-strand breaks (DSBs) that arise between repeated sequences (10,13,14). During SSA in S. cerevisiae, DSBs are resected 5′ to 3′ to reveal single-stranded homologous sequences ( Figure 1). Following Rad52-and Rad59-dependent annealing of the homologous sequences, the 3′ single-stranded DNA ends are nonhomologous to the new flanking regions, and must be cleaved in order to complete repair of the broken strands. The Rad1-Rad10 endonuclease and Msh2-Msh3 mismatch recognition complex are required for cleaving 3′ single-stranded nonhomologous tails on either side of the annealed region (15)(16)(17)(18)(19) NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript been removed, SSA is completed by DNA synthesis initiated off of the newly cleaved 3′ ends followed by ligation (reviewed in 10).Rad1-Rad10 is a structure-specific endonuclease that functions in both nucleotide excision repair (NER) and homologous recombination (10,11,19,20). The significance of the role of Rad1-Rad10 in recombination is demonstrated by the severe developm...

Increased Meiotic Crossovers and Reduced Genome Stability in Absence of Schizosaccharomyces pombe Rad16 (XPF)

“…We see similar fragmentation phenotypes for rhp14Δ XPA , but not for rad13Δ XPG . This agrees with data showing that XPA and XPF have functions independent of XPG and other NER proteins (Paques and Haber 1999;Lyndaker and Alani 2009) and implicates XPA and XPF in a distinct meiotic function.…”

“…This contrasts with budding yeast in which Rad14 XPA , the XPF loading factor, is not required for CPT resistance (Vance and Wilson 2002). Instead, Sc Slx4 and Saw1 are proposed to provide an alternative XPF loading complex, and Slx4 with Slx1 forms another structure-specific endonuclease (Lyndaker and Alani 2009;Schwartz and Heyer 2011). In fission yeast, Slx4-Slx1 endonuclease is linked to rDNA maintenance via a Rad51-independent recombination mechanism (Coulon et al 2006), but so far there is no evidence that Slx4 and Saw1 affect Rad16 XPF in S. pombe.…”

“…Finally, we observed sensitivity to hydroxyurea (HU) in rad16-249 and rhp14Δ mutants, but again not in rad13Δ. HU causes fork stalling due to nucleotide depletion, and restart occurs via recombination-based mechanisms (Meister et al 2007;Lambert et al 2010;Sabatinos et al 2012).Slx4 and Saw1 are proposed to function as scaffolds that assemble XPF and other structure-specific endonucleases (Lyndaker and Alani 2009;Kashiyama et al 2013;Li et al 2013;Wan et al 2013). In contrast to budding yeast (Flott et al 2007;Li et al 2008), neither slx4Δ nor saw1Δ is sensitive to UV or MMS in fission yeast (Figure S3 and (Coulon et al 2006).…”

“…Slx4 and Saw1 are proposed to function as scaffolds that assemble XPF and other structure-specific endonucleases (Lyndaker and Alani 2009;Kashiyama et al 2013;Li et al 2013;Wan et al 2013). In contrast to budding yeast (Flott et al 2007;Li et al 2008), neither slx4Δ nor saw1Δ is sensitive to UV or MMS in fission yeast (Figure S3 and (Coulon et al 2006).…”

A Functional Cancer Genomics Screen Identifies a Druggable Synthetic Lethal Interaction between MSH3 and PRKDC

“…1-4 ). There is accumulating circumstantial evidence suggesting a role for the MSH2-MSH3 complex in DSB repair (39)(40)(41)(42)(43). For instance, RNAi-mediated MSH3 depletion has recently been shown to result in substantially delayed RAD51 loading after 2-Gy ionizing radiation ( 25 ).…”