The Genom of Homo sapiens.pdf

450 STANKIEWICZ ET AL.ate DNA rearrangements, perhaps by stimulating doublestrandbreaks (DSB). In addition, the recombination ofnonhomologous sequences from the proximal/distalflanking regions, and the insertion of short sequencestretches at the recombination breakpoints, are both consistentwith the mechanism of nonhomologous end joining(NHEJ) (Inoue et. al. 2002). Of interest, preliminary dataindicate that at least some of the PLP1 duplication breakpointsare also located within the intervals containingLCR-PMDA and LCR-PMDB.Results supporting the involvement of genome architecturein nonrecurrent chromosome aberrations were obtainedwhen analyzing the breakpoints of 18 unusualsized SMS deletions in 17p11.2-p12. We identified sevennovel LCRs, which we termed LCR17ps. LCR17pA-Gare highly homologous (~98%), and their sizes vary between23 and 383 kb (Stankiewicz et al. 2003b). Remarkably,LCRs including CMT1A-REPs, SMS-REPs,LCR17ps, and RNU3-REPs (Gao et al. 1997) constitute>23% of the genome sequence in proximal 17p—an experimentalobservation two- to fourfold higher than predictionsbased on virtual analysis of the genome. Interestingly,64% of analyzed breakpoints within 17p11.2occur in these LCRs (Stankiewicz et al. 2003b).For chromosome deletions with both breakpoints mappingwithin nonhomologous copies of LCRs, or thosewith one breakpoint mapping within an LCR and theother in LCR-free unique DNA sequence, we proposedthat the deletion is stimulated, but not mediated, by theLCR(s) and may occur via either NAHR utilizing smallrepeat segments or by NHEJ. Deletions in which breakpointsdid not involve LCRs may occur through NHEJbetween repeat-free DNA fragments (Inoue et al. 2002;Stankiewicz et al. 2003b). NAHR between palindromicLCRs has been proposed also as a mechanism responsiblefor frequent deletions involving subtelomeric regionsof chromosome 1p36 (Ballif 2003).TranslocationsTo date, only a few constitutional reciprocal chromosometranslocation breakpoints have been shown to be associatedwith LCRs (Kehrer-Sawatzki et al. 1997; Kurahashiet al. 2000; Edelmann et al. 2001; Giglio et al.2002). Recently, we demonstrated that 7/8 analyzedbreakpoints of chromosome translocation involving chromosome17p11.2-p12 were associated with higher-ordergenomic architectural features such as LCRs and/or(peri)centromeric heterochromatin (Stankiewicz et al.2003b). Similarly, Spiteri et al. (2003) reported that out of14 different reciprocal translocations involving chromosome22q11, 5 breakpoints mapped within LCR22-3 andan additional 4 occurred within the vicinity of otherLCR22s. Interestingly, 18 partner chromosome breakpointsmapped within the most telomeric bands(Stankiewicz et al. 2003b; Spiteri et al. 2003). These datafurther indicate that higher-order genomic architecturealso plays a significant role in the origin of nonrecurrentchromosome rearrangements.Marker Chromosomes and JumpingTranslocationsLCR-related genome architecture appears to be involvedin the origin of other nonrecurrent chromosome aberrations,such as marker chromosomes (Stankiewicz et al. 2001b)and jumping translocations (Stankiewicz et al. 2003a).MOLECULAR MECHANISMS OFGENOMIC DISORDERSDepending on the location and orientation of nonallelicLCR copies, the stimulated NAHR may involve the samechromatid, different chromatids on the same chromosome,different chromosome homologs, or even differentchromosomes. As a result, a wide variety of chromosomeaberrations may arise (for review, see Stankiewicz andLupski 2002a). Most often, unequal exchange betweendirectly (tandemly) oriented LCRs is predicted to result indeletion and duplication, whereas the recombination usinginverted copies as recombination substrates wouldlead to the inversion of the DNA segment flanked by therepeats (Lupski 1998).Unequal Crossing-overNAHR between paralogous LCR copies (unequal crossing-over)within one chromosome (intrachromosomal) orbetween different chromosomes (interchromosomal) hasbeen proven to be a molecular mechanism resulting in genomicdeletions and duplications in several genomic disorders(Pentao et al. 1992; Reiter et al. 1996; Edelmann etal. 1999; Amos-Landgraf et al. 1999; Dorschner et al.2000; Shaw et al. 2002; Bayés et al. 2003).Double-strand DNA Breaks InitiateRecombination EventsDNA sequence analysis and comparison between paralogousLCRs in regions of strand exchange revealed thatcrossovers occur within selected stretches of perfect sequenceidentity (Lagerstedt et al. 1997; Reiter et al. 1998;Lopes et al. 1999). The exact molecular mechanism andrequirements for strand exchange remain unknown. It isthought that the minimal efficient processing segment(MEPS), or stretch of sequence identity required by thecellular recombination machinery, is probably ~200–300bp in mitosis (Waldman and Liskay 1988) and potentially~300–500 bp in meiosis (Reiter et al. 1998). Evidence forgene conversion, consisting of an admixture of sequencederived from two recombined LCRs, has been observedin several genomic disorders. This finding suggests thatDSBs initiate NAHR because the DSB-repair process utilizesallelic homologs (or nonallelic paralogs in the caseof NAHR) as the template to reconstruct the sequencethat was lost in the DSB and subsequent exonuclease excision(Inoue and Lupski 2002). Double exchange withinLCRs may also lead to their homogenization, thus in-