Break-induced replication: A review and an example in budding yeast

Abstract

Break-induced replication (BIR) is a nonreciprocal recombinationdependent replication process that is an effective mechanism to repair a broken chromosome. We review key roles played by BIR in maintaining genome integrity, including restarting DNA replication at broken replication forks and maintaining telomeres in the absence of telomerase. Previous studies suggested that gene targeting does not occur by simple crossings-over between ends of the linearized transforming fragment and the target chromosome, but involves extensive new DNA synthesis resembling BIR. We examined gene targeting in Saccharomyces cerevisiae where only one end of the transformed DNA has homology to chromosomal sequences. Linearized, centromere-containing plasmid DNA with the 5 end of the LEU2 gene at one end was transformed into a strain in which the 5 end of LEU2 was replaced by ADE1, preventing simple homologous gene replacement to become Leu2 ؉ . Ade1 ؉ Leu2 ؉ transformants were recovered in which the entire LEU2 gene and as much as 7 kb of additional sequences were found on the plasmid, joined by microhomologies characteristic of nonhomologous end-joining (NHEJ). In other experiments, cells were transformed with DNA fragments lacking an ARS and homologous to only 50 bp of ADE2 added to the ends of a URA3 gene. Autonomously replicating circles were recovered, containing URA3 and as much as 8 kb of ADE2-adjacent sequences, including a nearby ARS, copied from chromosomal DNA. Thus, the end of a linearized DNA fragment can initiate new DNA synthesis by BIR in which the newly synthesized DNA is displaced and subsequently forms circles by NHEJ. D uring the past several years, some old ideas about how recombination occurs have received strong experimental support. Meselson and Weigle (1) first proposed that crossingover could be explained by a break-copy mechanism in which one end of a double-strand break (DSB) could invade an intact linear template molecule and initiate new DNA synthesis that could proceed to the end of the chromosome template. In essence, a recombination event led to the establishment of a unidirectional replication fork. Skalka (2) provided a more molecular view of this idea (a replicator's view of recombination, as she called it) to explain phage recombination. Mosig (3, 4) made a similar proposal to account for late DNA replication in phage T4. Formosa and Alberts (5) provided a key in vitro experimental demonstration for the formation of a replication fork by recombination. More recent studies by George and Kreuzer (6) of DSB-induced recombination, controlled by phage T4 genes in Escherichia coli have supported the idea that recombination leads to extensive replication. Similarly, recent experiments by Motamedi et al. (7) and by Kuzminov and Stahl (8) with phage have provided strong evidence that a major pathway to generate crossing-over involves extensive replication during break-copy recombination.These ideas were applied by Kogoma (9, 10) to explain origin-independent, recombination-dependent replication of the E. ...

Rad22Rad52-dependent Repair of Ribosomal DNA Repeats Cleaved by Slx1-Slx4 Endonuclease

“…This DNA break may be processed by Rad22-dependent HR pathway ( Figure 6A). This pathway may be analogous to the Rad52-dependent, Rad51-independent pathway of break-induced replication (BIR) described in S. cerevisiae (Malkova et al, 1996;Kraus et al, 2001). This mechanism might involve the activity of DNA helicases that unwind duplex DNA and thereby generate a substrate for Rad22-dependent strand annealing, possibly coupled with the presence of nicks or single strand gaps in the targeted rDNA repeat.…”

Minding the gap: The underground functions of BRCA1 and BRCA2 at stalled replication forks

“…3). BIR was first described as a RAD51-independent error-prone DSBR pathway and is known to mediate several types of chromosomal instability in yeast [55][56][57][58]. BIR is as processive as conventional chromosomal replication and it therefore probably entails formation of a replication fork at the recombination joint [59] (Fig.…”

XRCC4 in G1 suppresses homologous recombination in S/G2, in G1 checkpoint-defective cells

“…Third, mice deficient in both NHEJ and p53, develop lymphomas, resulting from rearrangements initiated by V(D)J recombination-activating protein (RAG)-induced DNA cleavage and involving a break-induced replication (BIR) pathway (Vanasse et al, 1999;Difilippantonio et al, 2002;Zhu et al, 2002). BIR is a DSB repair process requiring sequence homology and in part Rad51-dependent in yeast (Kraus et al, 2001;Malkova et al, 2005).…”