Figure 1. The DSBR repair pathways.
The chromatids are shown as double-stranded molecules with arrows at the 3’ ends. The broken chromatid is colored blue and the intact template chromatid is red. Dotted lines indicate newly-synthesized DNA. Regions of heteroduplex DNA (hetDNA) are outlined by black boxes. All pathways are initiated by invasion of one processed broken end into the unbroken chromatid, forming a D-loop. (A) One-ended Synthesis-dependent strand annealing (SDSA). Following DNA synthesis primed by the invading 3’ end, the invading end dissociates from the intact molecule, and re-anneals with the second broken end. The net result is an NCO event with hetDNA extending uni-directionally from the break. (B) Two-ended SDSA. In this mechanism, following DNA synthesis from the invading end, the other broken end pairs with the D-loop and initiates DNA synthesis. Before ligation to generate a dHJ intermediate, the invading end disengages from the template and re-pairs with the other broken end. The net result is a single chromatid with a bi-directional heteroduplex that has a strand switch at the site of the initiating DSB. (C) Double Holliday junction (dHJ) intermediate. Following DNA synthesis from one invading end, the second broken end pairs with the D-loop (second-end capture). This intermediate can be dissolved by migrating the two junctions inwards, followed by decatenation; this pathway results in a NCO with a bi-directional heteroduplex, identical to the product of the two-ended SDSA mechanism. Alternatively, it can also be resolved by cutting the junctions symmetrically to generate NCOs (cuts at arrows marked 1, 2, 3, and 4 or 5, 6, 7, and 8), or asymmetrically (cuts at arrows marked 2, 4, 5, and 6 or 1, 3, 7 and 8) to generate COs. For both types of resolution, the heteroduplexes are located on different chromatids, flanking the DSB site, and pointing in opposite directions. Note that cuts at positions 1, 3, 7, and eight reflect nick-directed resolution of the junctions. (D) Break-induced replication (BIR). In this pathway, one broken end invades the intact template and copies DNA sequences by conservative replication to the end of the template. The other broken end is lost. Except for the initial strand invasion, heteroduplex intermediates are not relevant to this pathway.