Double Strand Break-
Induced Replication
The repair of broken chromosomes by homologous recombination may occur in several ways (See Introduction). If both ends at the break have homology to sequences on an unbroken chromosome that can serve as a template, then repair may proceed by gene conversion. However, in some cases only one end of the DSB may have, at or near its end, homology with sequences elsewhere in the genome. In this case a single stranded tail can invade a homologous duplex DNA molecule and prime DNA replication. This leads to duplication of one chromosome arm.

Such a situation prevails in a haploid or hemizygous chromosomes in the G1 stage of the cell cycle, or in special situations such as when a cell lacks the telomerase enzyme that maintains chromosome termini. In both of these cases, an alternative mechanism of repair, known as break-induced replication (BIR) may be able to restore a telomere to the broken chromosome and thus preserve its integrity.

In S. cerevisiae, events consistent with BIR have been directly demonstrated in several ways. First, when HO endonuclease is used to cleave off the end of one chromosome in a haploid, repair can occur by creating a non-reciprocal translocation, in which a 70 bp sequence centromere-proximal to an HO-induced DSB appears to invade a homologous sequence located on the other chromosome arm, 30 kb from its telomere. Replication from this site produced a non-reciprocal translocation in which the 30 kb region was found distal to the end produced by HO cleavage.

Similar kinds of events have been demonstrated in yeast transformation experiments, where the end of a linearized fragment apparently established a replication fork that could proceed several hundred kb to a chromosome end. These events appear to be analogous to the maintenance of yeast telomere regions in the absence of a functional telomerase.
A linear DNA sequence derived from a plasmid containing a centromere and flanking sequences homologous to the chromosome is transformed into yeast. This initiates BIR leading to the formation of an isochromosome (inverted arms).

Genetic Requirements. BIR has also been documented in a diploid experiencing a single HO endonuclease-induced DSB on one chromosome, where repair by gene conversion using a homologous chromosome as a template was prevented by a rad51 mutation. In the absence of yeast's strand exchange protein, Rad51p, gene conversion is abolished and repair of the broken chromosome can occur by a BIR mechanism that causes all markers distal to the site of the DSB to become homozygous.

Although BIR is not RAD51-dependent, it is RAD52-dependent. In the absence of RAD52 a broken chromosome is almost always lost. To further investigate the mechanism of BIR, we have examined the effects of deleting most of the other members of the RAD52 epistasis group. We found that gene conversion is also prevented when RAD54, RAD55 and RAD57 are deleted but BIR occurs, as with rad51 cells.

Gene conversion was not significantly affected when RAD50, RAD59, TID1, SRS2 or SGS1 were deleted. Various double mutants largely eliminate both gene conversion and BIR, including rad51 rad50, rad51 rad59 and rad54 tid1. These results suggest that there is a RAD51, RAD54-independent BIR pathways that requires RAD50, RAD59 and TID1.