In the pairing-site model, specialized regions on each chromosome function to establish meiotic homolog pairing. Analysis of these sites could provide insights into the mechanism used by Drosophila females to form a synaptonemal complex (SC) in the absence of meiotic recombination. These specialized sites were first established on the X chromosome by noting that there were barriers to crossover suppression caused by translocation heterozygotes. These sites were genetically mapped and proposed to be pairing sites. By comparing the cytological breakpoints of third chromosome translocations to their patterns of crossover suppression, we have mapped two sites on chromosome 3R. We have performed experiments to determine if these sites have a role in meiotic homolog pairing and the initiation of recombination. Translocation heterozygotes exhibit reduced gene conversion within the crossover-suppressed region, consistent with an effect on the initiation of meiotic recombination. To determine if homolog pairing is disrupted in translocation heterozygotes, we used fluorescent in situ hybridization to measure the extent of homolog pairing. In wild-type oocytes, homologs are paired along their entire lengths prior to accumulation of the SC protein C(3)G. Surprisingly, translocation heterozygotes exhibited homolog pairing similar to wild type within the crossover-suppressed regions. This result contrasted with our observations of c(3)G mutant females, which were found to be defective in pairing. We propose that each Drosophila chromosome is divided into several domains by specialized sites. These sites are not required for homolog pairing. Instead, the initiation of meiotic recombination requires continuity of the meiotic chromosome structure within each of these domains. M EIOTIC recombination usually occurs between sophila have supported the view that SC formation ocsimilar or identical sequences on homologous curs prior to DSB formation (Jang et al. 2003). chromosomes. In most organisms, at least part of the The presence of single-strand tails at DSB sites promeiotic recombination pathway occurs within the convides a mechanism for homology searching and chromotext of the synaptonemal complex (SC), which holds some alignment (Roeder 1997). In organisms like Droaligned homologous chromosomes together along their sophila and C. elegans, however, another mechanism entire lengths (von Wettstein et al. 1984). Surprisaside from recombination must exist to precisely align ingly, organisms can be classified into at least two types homolgous chromosomes during meiosis. Indeed, DSBon the basis of the relationship of double-strand-break independent mechanisms for aligning meiotic chromo-(DSB) formation to the SC. In Saccharomyces cerevisiae, somes appear to be widespread. Similar to Drosophila DSB formation occurs prior to, and is required for, SC and C. elegans, homolog pairing in fission yeast involves a formation (Padmore et al. 1991). A similar course of DSB-independent component (Ding et al. 2004). While events occurs in...