mitotic cells was counted in at least five discs. Each experiment was performed three times. Database Searches Domain searches were conducted at four sites: NCBI (http:// www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml), Prosite (http:// ca.expasy.org/prosite/), Superfamily (http://supfam.cs.bris.ac. uk/SUPERFAMILY/), and Pfam (http://pfam.sanger.ac.uk/ search). Blast searches against Drosophila and other insect species as performed at FlyBase (http://flybase.bio.indiana.edu/blast/). Blast searches against the human genome was performed at NCBI (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi). As comparisons among the 12 Drosophila genomes indicated that the MU2 amino acid sequence had diverged rapidly, blast searches were done using BLOSUM45 and filters turned off. The cutoff E value was set at 0.001. Supporting Information Figure S1 Distribution of MU2 in the imaginal discs. Imaginal discs were dissected from wandering third instar larvae. The discs were fixed in 4% paraformaldehyde and immunostained with mouse anti-MU2 antiserum. (A) Eye antennal imaginal disc (B) wing imaginal disc and (C) leg imaginal disc. MU2 is distributed evenly over the discs. Found at: doi:10.1371/journal.pgen.1000473.s001 (47.2 MB TIF) References 1. Cortes-Ledesma F, Aguilera A (2006) Double-strand breaks arising by replication through a nick are repaired by cohesin-dependent sister-chromatid exchange. EMBO Rep 7: 919–926. 2. Paques F, Haber JE (1999) Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 63: 349–404. 3. Soulas-Sprauel P, Rivera-Munoz P, Malivert L, Le Guyader G, Abramowski V, et al. (2007) V(D)J and immunoglobulin class switch recombinations: a paradigm to study the regulation of DNA end-joining. Oncogene 26: 7780–7791. 4. Downey M, Durocher D (2006) Chromatin and DNA repair: the benefits of relaxation. Nat Cell Biol 8: 9–10. 5. 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