The Genom of Homo sapiens.pdf

GENOME ARCHITECTURE AND GENOMIC DISORDERS 451ABFigure 4. Novel junction fragments from reciprocal recombination were identified in SMS and dup(17)(p11.2p11.2) patients. (A) Sequenceprediction of novel junction fragments from recombinant SMS-REPs. A portion of the KER gene cluster of distal (dist) andproximal (prox) SMS-REPs are shown with the horizontal filled rectangles depicting homology segments. A 9.7-kb fragment fromthe distal SMS-REP and an 11.5-kb fragment from the proximal copy will be detected when genomic DNA is double-digested withBamHI and SpeI and hybridized with a 906-bp probe (a short horizontal bar under the distal SMS-REP). In addition, a 6.9-kb junctionfragment from patients with SMS deletion and a 14.5-kb junction fragment in its reciprocal duplication from dup(17)(p11.2p11.2)patients are predicted when the strand exchange events occur in block C and centromeric to the distal specific BamHI site. (B) Thepredicted novel junction fragments were detected in SMS patients and dup(17)(p11.2p11.2) patients. A 6.9-kb junction fragment wasobserved in a patient (429) with the SMS common deletion, but not in her unaffected parents. A 14.5-kb junction fragment was observedin a dup(17)(p11.2p11.2) patient (1364) but not in his unaffected mother and siblings. The novel junction fragments are indicatedby the arrowheads. (Modified from Bi et al. 2003.)creasing their similarity and the potential rate of subsequentNAHR events between them (Blanco et al. 2000;Saunier et al. 2000; Hurles 2001).Positional Preference for Strand ExchangeClustering of breakpoints has been observed for thefew LCR/NAHR-mediated events studied at the nucleotidesequence level. HNPP and CMT1A recombinationproduct characterization has revealed, respectively,557-bp and 2-kb regions of strand exchange at recombinationhot spots (Reiter et al. 1998; Lopes et al. 1999).Similar positional recombination hot spots have beenidentified also within LCRs associated with AZFa(azoospermia factor a) microdeletion (Kamp et al. 2000),neurofibromatosis type 1 (Jenne et al. 2001; López-Correaet al. 2001), and Williams-Beuren syndrome (Bayéset al. 2003). Recently, we have identified similar strandexchange clustering in SMS-REPs, in which ~50% ofbreakpoints clustered in a 12-kb region of the ~170-kbhomology intervals within SMS-REPs. As anticipated,the same 12-kb interval is the preferred region for strandexchange in the reciprocal crossover resulting indup(17)(p11.2p11.2) (Fig. 4). Interestingly, we identifiedinverted repeats of ~2 kb in size directly flanking this hotspot. We hypothesize that these repeats, or the large loopsecondary DNA structures missing in the distal SMS-REP, may make the hot spot region more sensitive toDSBs, and therefore stimulate homologous recombination(Bi et al. 2003).CONCLUSIONSGenomic disorder-associated DNA rearrangements inproximal chromosome 17p are an excellent model to investigatethe role of genome architecture in constitutional,evolutionary, and somatic rearrangements (Fig. 5).Molecular studies of the CMT1A duplication, the SMSdeletion, their reciprocal recombination products, andother disease-causing chromosomal rearrangements haverevealed common mechanisms for genomic disorders.The rearrangements are not random events, but rather reflectgenome architecture. This genome architecture consistsof region-specific LCRs that act as substrates forNAHR (unequal crossing-over) and thus contribute to thesusceptibility to DNA rearrangements and genomic instability.The LCRs appear to have arisen recently duringprimate speciation through serial segmental duplicationsand likely play a role in genome evolution. The humangenome has evolved an architecture that may make us asa species more susceptible to rearrangements causing genomicdisorders. Because LCRs comprise a significantportion of the human genome, these recombination-baseddisorders contribute substantially to genetic disease burden,and the number of conditions that are recognized asgenomic disorders continues to grow.