New and old ways to control meiotic recombination

Abstract

The unique segregation of homologs, rather than sister chromatids, at the first meiotic division requires the formation of crossovers (COs) between homologs by meiotic recombination in most species. Crossovers do not form at random along chromosomes. Rather, their formation is carefully controlled, both at the stage of formation of DNA double-strand breaks (DSBs) that can initiate COs and during the repair of these DSBs. Here, we review control of DSB formation and two recently recognized controls of DSB repair: CO homeostasis and CO invariance. Crossover homeostasis maintains a constant number of COs per cell when the total number of DSBs in a cell is experimentally or stochastically reduced. Crossover invariance maintains a constant CO density (COs per kb of DNA) across much of the genome despite strong DSB hotspots in some intervals. These recently uncovered phenomena show that CO control is even more complex than previously suspected.

Figure 1. Meiotic recombination initiation in the fission yeast S. pombe

Programmed DNA double-strand breaks (DSBs) initiated by Rec12 (Spo11 in other species) during meiosis are efficiently repaired by homologous recombination with high fidelity (for simplicity only one chromatid from each homolog is depicted). Rec12 is aided by several meiotic break proteins to localize and form DSBs. In S. cerevisiae the MRX complex (Mre11, Rad50, Xrs2) is required for DNA breakage and repair, whereas in S. pombe MRN (Mre11, Rad50, Nbs1) is needed only for repair. Rec12, covalently linked to the 5' ends of the DSB, is clipped off attached to short oligonucleotides (~15–45 long) by MRN in conjunction with Ctp1 (Sae2 in S. cerevisiae). The 5' end is further resected by Ctp1 or Exo1 in conjunction with MRN, resulting in a free 3' DNA end. Rad51 and Dmc1, along with numerous accessory proteins, bind the ssDNA end and facilitate invasion of an intact duplex DNA with homology to the invading end. Synthesis of DNA from the end uses the invaded DNA as a template for repair. See Figure 2 for further reactions.

Figure 2. Pathways of meiotic DSB repair

During meiosis chromosomes are first replicated (step 1) and the identical sister chromatids (red and blue double lines indicate duplex DNA) are linked together by meiosis-specific cohesins (step 1, gold lines) and additional proteins that form axial elements (step 2, purple ovals). Pairing of homologs leads to formation of the synaptonemal complex (step 3, yellow bars); in D. melanogaster, for example, synapsis occurs independently of DSBs, while in S. cerevisiae synapsis would not occur until step 8. Recombination is initiated by programmed DSBs by Rec12 or Spo11 (Figure 1) and numerous partners (step 4, green circles). The now covalently bound Rec12 or Spo11 is removed and the DNA end is resected to create free 3' DNA ends (step 5). The 3' DNA ends invade either the homolog (step 6) or the sister chromatid (step 6a) to create a displacement loop (D-loop), which is extended by DNA synthesis primed by the invading 3' end (see Figure 1 for details). Rad51- or Dmc1-promoted annealing of the other 3' end (“second end capture,” step 7) and ligation of ends forms a double Holliday junction (dHJ; step 8). A single HJ (sHJ; step 7b) is formed if the D-loop is cleaved before the second end anneals. HJ resolution yields a crossover (CO) or non-crossover (NCO), depending on the orientation of cleavage of the HJ(s) (white arrowheads, step 9). If, however, the D-loop is dissociated and the invading end, previously extended by DNA synthesis, anneals with the other DSB end (step 7a), a NCO is formed; this repair is called synthesis-dependent strand annealing (SDSA). Crossover control can act at steps 6, 7, or 9.

Figure 3. Two mechanisms to distribute crossovers across chromosomes

(a) Crossover homeostasis observed in S. cerevisiae [5, 81, 60]. A crossover (CO) generated at one DSB (green zig-zag) inhibits nearby DSBs from generating another CO, a phenomenon known as crossover interference (COI; Box 1) (represented by yellow clouds; deeper color representing greater interference). Instead, these adjacent DSBs are repaired as non-crossovers (NCOs). The amount of DSBs may vary from cell to cell in meiosis: one with abundant DSBs (top diagram) has more NCOs than one with few DSBs (lower diagram), but the overall level of COs remains constant. Homeostasis is thought to arise from the same mechanism as COI and to occur in other species. (b) A different mechanism of crossover control, crossover invariance, observed in S. pombe [6]. S. pombe has intense DSB hotspots that are widely space across the genome but a nearly constant level of COs per kb of DNA. In other words, a genetic interval with a DSB hotspot has about the same frequency of COs as one of similar size without a DSB hotspot. At these DSB hotspots, intersister (IS) repair is more frequent than interhomolog (IH) repair, but away from hotspots DSB repair is mostly or all IH. Since IS repair does not yield genetically observable COs, the amount of COs from hotspots is roughly equal to the COs generated away from hotspots, resulting in the observed crossover invariance.