Supporting Methods

Searches for Putative Sequences Involved in Chromosome Rearrangement. Searches for common motives in the 200-bp region surrounding breakpoints were performed by using the following two programs: MEME (http://meme.sdsc.edu/meme/website/intro.html) (1) and MULTALIN (http://prodes.toulouse.inra.fr/multalin/multalin.html) (2). In the same regions, consensus sequences were searched by using the PATTERN program (http://www.infobiogen.fr/services/analyseq/cgi-bin/patternn_in.pl) (3). In addition, matches were searched for Chi-like sequences (GC[A/T]GG[A/T]GG) (4), minisatellite core sequences (5), alternating purine/pyrimidine and polypurine or polypyrimidine sequences (6 , 7), Ig heptamer (GATAGTG) (8), and translin-binding sites (ATGCAG and GCCC[A/T][G/C] [A/T] ((9). Finally, the presence of topoisomerase II cleavage sites was also investigated {topoIIv, [G/A]N[T/C]NNCNNG[T/C]NG[G/T][T/C] (10); topoIId, GTN[T/A]A[C/T]ATTNATNN [A/G] (11, 12); and topoIIi, [T/C][T/C]CNTA[C/G][C/T]CC[T/G][T/C][T/C]TNNC}(13).

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