A palindrome-driven complex rearrangement of 22q11.2 and 8q24.1 elucidated using novel technologies

Abstract

Constitutional translocations at the same 22q11.21 low copy repeat B (LCR-B) breakpoint involved in the recurrent t(11;22) are relatively abundant. A novel 46,XY,t(8;22)(q24.13;q11.21) rearrangement was investigated to determine whether the recurrent LCR-B breakpoint is involved. Investigations demonstrated an inversion of the 3Mb region typically deleted in patients with the 22q11.2 deletion syndrome. The 22q11.21 inversion appears to be mediated by low copy repeats, and is presumed to have taken place prior to translocation with 8q24.13. Despite predictions based on inversions observed in other chromosomes harboring low copy repeats, this 22q11.2 inversion has not been observed previously. The current studies utilize novel laser microdissection and MLPA (multiplex ligation-dependent probe amplification) approaches, as adjuncts to FISH, to map the breakpoints of the complex rearrangements of 22q11.21 and 8q24.21. The t(8;22) occurs between the recurrent site on 22q11.21 and an AT-rich site at 8q24.13, making it the fifth different chromosomal locus characterized at the nucleotide level engaged in a translocation with the unstable recurrent breakpoint at 22q11.21. Like the others, this breakpoint occurs at the center of a palindromic sequence. This sequence appears capable of forming a perfect 145 bp stem-loop. Remarkably, this site appears to have been involved in a previously reported t(3;8) occurring between 8q24.13 and FRA3B on 3p14.2. Further, the fragile site-like nature of all of the breakpoint sites involved in translocations with the recurrent site on 22q11.21, suggests a mechanism based on delay of DNA replication in the initiation of these chromosomal rearrangements.[Supplemental material is available online at www.genome.org] The 22q11.21 region represents a hot spot for nonrandom chromosomal aberrations, including deletions, translocations, supernumerary chromosomes, and, less frequently, interstitial duplications (Lindsay et al. 1995;Edelmann et al. 1999;Ensenauer et al. 2003;Meins et al. 2003;Hassed et al. 2004;Portnoi et al. 2005;Yobb et al. 2005). These rearrangements are associated with genetic disorders including the 22q11.21 deletion syndrome, supernumerary der(22)t(11;22) syndrome (Emanuel syndrome), cat eye syndrome (CES), and, occasionally, Opitz syndrome (OS) (for review, see Driscoll and Emanuel 1998). The breakpoints of these rearrangements are frequently localized to a class of chromosome-specific repeat sequences known as low-copy repeats (LCRs) or segmental duplications. Each LCR on 22q11 consists of cluster of sequence modules that are repeated in other chromosome 22 LCRs with 97%-98% sequence identity. LCRs differ from one another in their sequence module content and organization.A total of eight LCRs have been identified within 22q11 (LCRs A to H, proximal to distal), with most constitutional rearrangements involving LCRs A through D, or the 3 Mb typically deleted region (TDR) (Edelmann et al. 1999;Shaikh et al. 2000).LCR-B contains a recurrent translocation breakpoint site that i...

Chromosomal instability mediated by non-B DNA: Cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans

“…t(11;22) is also detectable as de novo translocations in sperm from normal healthy males at frequencies of 10 À4 to 10 À5 , but not in other mitotic cells (Kurahashi and Emanuel 2001). Similar PATRR sequences have been found at the breakpoints of t(17;22)(q11;q11) (KehrerSawatzki et al 1997;Kurahashi et al 2003), t(4;22)(q35;q11) (Nimmakayalu et al 2003), t(1;22)(p21.2;q11) (Gotter et al 2004), and t(8;22)(q24.13;q11.21) (Gotter et al 2007). It is therefore accepted that PATRRs can cause recurrent and nonrecurrent chromosomal translocations in humans.…”

Two sequential cleavage reactions on cruciform DNA structures cause palindrome-mediated chromosomal translocations

“…Thus, we proposed that the palindromic sequences form a cruciform conformation in vivo, and this conformation could induce DNA breakage that results in illegitimate joining, leading to a reciprocal translocation. To date, more than five other translocation-associated PATRRs have been identified, suggesting that palindrome-mediated chromosomal translocations are one of the important pathways generating GCRs in humans [14][15][16][17][18] .…”

Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13)

“…Breakpoints in only a few constitutional rearrangements in individuals with normal phenotypes have been examined at the DNA sequence level. These include translocations t(11;22) (Kurahashi et al 2000(Kurahashi et al , 2007, the most common constitutional translocation in humans, in which junction fragments were identified, and other translocation events including t(1;22)(p21.2;q11.2) (Gotter et al 2004), t(4;22)(q35.1;q11.2) (Nimmakayalu et al 2003), and t(8;22)(q24.13;q11.21) (Gotter et al 2007). We have previously examined apparently balanced translocations in phenotypically normal individuals and found evidence that translocation junctions may show sequence inconsistency at the breakpoints created by addition of nucleotides and duplications (Gajecka et al 2006b).…”