Break-induced replication occurs by conservative DNA synthesis

Abstract

Break-induced replication (BIR) refers to recombination-dependent DNA synthesis initiated from one end of a DNA double-strand break and can extend for more than 100 kb. BIR initiates by Rad51-catalyzed strand invasion, but the mechanism for DNA synthesis is not known. Here, we used BrdU incorporation to track DNA synthesis during BIR and found that the newly synthesized strands segregate with the broken chromosome, indicative of a conservative mode of DNA synthesis. Furthermore, we show the frequency of BIR is reduced and product formation is progressively delayed when the donor is placed at an increasing distance from the telomere, consistent with replication by a migrating D-loop from the site of initiation to the telomere.H omologous recombination (HR) is an important mechanism to repair DNA double-strand breaks (DSBs) that occur spontaneously during cell growth or following exposure to DNA damaging agents (1). HR relies on the presence of a homologous duplex to template repair of the broken chromosome and is generally considered to be an error-free mechanism. However, HR can lead to a local loss of heterozygosity (LOH) if the recombining sequences are not identical, and to extensive LOH if repair is associated with a crossover between chromosome homologs. Furthermore, if a repeated sequence at an ectopic site is used as the sequence donor and recombination is associated with crossing over, translocations can occur (2, 3). When both ends of the DSB share homology with the donor duplex sequence, HR proceeds by a two-ended mechanism, such as DSB repair or synthesis-dependent strand-annealing (SDSA) (4-6). However, if coordination of the two ends is not maintained or only one end of the break is available, such as at a critically short telomere, repair can occur by break-induced replication (BIR) (7). In this case, following strand invasion replication occurs to the end of the chromosome to generate a stable repaired product (8,9). This process can cause very long gene conversion tracts and significant LOH, and nonreciprocal translocation if invasion occurs at a dispersed repeated sequence (10).The repair of DSBs by HR requires the 5′-3′ nucleolytic degradation of the DNA ends to form invasive 3′ single-stranded DNA (ssDNA) tails (1). The 3′ ssDNA tail created by end resection is bound by Rad51 to form a nucleoprotein filament that searches for homology and promotes pairing between the ssDNA bound by Rad51 and complementary sequence in the donor duplex forming a D-loop intermediate. The invading 3′ end is then used to prime DNA synthesis templated by the donor sequence. If the invading 3′-tail is displaced by helicases and anneals with the other end of break, repair by SDSA results in noncrossover products. If the second end of the break is captured by the D-loop, a double Holliday junction can be generated after DNA repair synthesis and ligation. Double Holliday junctions can either be dissolved by the Sgs1 helicase and Top3 topoisomerase to form noncrossover products or resolved by endonucleases to generate cr...

PolySUMOylation by Siz2 and Mms21 triggers relocation of DNA breaks to nuclear pores through the Slx5/Slx8 STUbL

“…The DSB survival assay is described in the Supplemental Material; the BIR assay was performed and the frequency of recombinants was calculated as previously described (Donnianni and Symington 2013).…”

The Role of Double-Strand Break Repair Pathways at Functional and Dysfunctional Telomeres

“…Strand invasion could also involve a telomere of another chromosome, and, in both cases, the invading end could be involved in break-induced replication (BIR) (Fig. 4D) (Donnianni and Symington 2013;Saini et al 2013;Wilson et al 2013;Mehta and Haber 2014).…”

DNA Repair Mechanisms and Their Biological Roles in the Malaria Parasite Plasmodium falciparum

“…3L). BIR can cause extensive loss of heterozygosity in diploids (60). In Plasmodium, BIR is one mechanism that is believed to generate novel var sequences (see below).…”