Fig. 2. Development of nodules from leptotene into zygotene. (A) An early leptotene spermatocyte nucleus with the stage defined by the earliest formation of SYCP3 chromosome-core segments (FITC, green). By the internal clock of the progression from zero to 250-plus RAD51-DMC1 foci (Rhodamine, red foci), this nucleus with 100 foci is still developing RAD51-DMC1 sites. The foci are usually connected to a core segment and they are the centres of diffuse H2AX domains (Rhodamine, red). (B) Reorganization of H2AX domains (FITC, green). At a slightly later leptotene stage, the spherical domains rearrange into flare-shaped domains. (C) Alignment of 230 foci and associated H2AX flares (FITC, green). (D,E) Zygotene chromosome cores. Foci of the unpaired cores and recently paired cores (green) are associated with H2AX (Rhodamine, red domains) but the foci of fully synapsed cores have no, or strongly reduced, H2AX domains. Presumably annealing and/or repair has been completed.