Genomic Architecture And The Generation Of Terminal Deletions Of 1p36

Repetitive DNA Sequence Elements

In recent years, numerous examples in the literature have documented repetitive DNA sequence elements as promoters of aberrant homologous recombination and DNA DSBs (83,84). This is evidenced by the vast number of cases in which repetitive DNA sequence elements are found at the breakpoints in constitutional chromosomal aberrations that cause genetic disease and in sporadic chromosomal abnormalities that cause cancer (83,84).

Presumably, aberrant homologous recombination between closely related repetitive DNA sequence elements (such as Alu and L1 sequences) can mediate these rearrangements without a prolonged period as a broken chromosome. In four subjects with apparently terminal deletions of 1p36, the breakpoints occurred in repetitive DNA sequence elements (55). This suggests that aberrant homologous recombination may have been involved in generating and/or stabilizing these terminal deletions. Aberrant homologous recombination between Alu elements has also been attributed to the generation of two subtle interstitial deletions of 16p that were initially thought to be simple chromosomal truncations (60,85). A similar situation has also been reported for a terminal deletion of 18q in which satellite III DNA sequences were located at the breakpoint (86).

Some repetitive DNA sequence elements have also been shown to be susceptible to genomic rearrangements including deletions (83,84). Microsatellite, minisatellite, and other short

Fig. 1. Mechanisms for stabilizing a broken chromosome. (A) Premeiotic or meiotic DNA damage generates a double-strand break that converts an intact normal chromosome into a broken, terminally deleted chromosome. Although DNA repair pathways could function to restore an intact normal chromosome (B), cell-cycle checkpoints may recognize the damaged chromosome and target the cell for an apoptotic pathway (C). Thus, neither of these two possible pathways (B or C) would be observed in subjects with monosomy 1p36 because a restored normal chromosome (B) would not produce a phenotype and an apoptotic cell (C) would simply not survive. However, a variety of competing DNA repair pathways could function to stabilize a broken chromosome. Terminal truncations could be formed by telomerase-mediated de novo addition of telomeric repeats or through telomerase-independent mechanisms such as break-induced replication (BIR) (D). (E) Stabilization could also occur by telomere capture forming a derivative chromosome through BIR. If more than one broken chromosome is present in the cell, single-strand annealing or nonhomologous end-joining (NHEJ) could also generate a nonreciprocal translocation. If the original telomere were captured, a true interstitial deletion could also be formed (F). Alternatively, DNA replication and NHEJ could occur (G), resulting in breakage-fusion-bridge cycles that generate inverted duplications and terminal deletions that in turn require stabilization (H). All of these pathways have been proposed in terminal deletions of 1p36. In addition, genomic architectural features, such as palindromic low-copy repeats in the subtelomeric region of 1p36, could result in nonallelic homologous recombination, creating a dicentric chromosome that breaks at a random location during anaphase (I). These types of random breaks could be a source of variable-sized broken chromosomes that are then stabilized by one of several competing double-strand break repair pathways. A similar set of DNA repair pathways that safeguard against genomic instability has been described in yeast systems. (Adapted from ref. 54.)

repetitive sequences are particularly susceptible to replication errors and can generate palindromic, hairpin structures that are prone to cleavage, resulting in DSBs and other chromosomal rearrangements (87-90). Because the breakpoints of four subjects with terminal deletions of 1p36 were shown to be located within repetitive DNA sequence elements, it is reasonable to suggest that some terminal deletions of 1p36 may have been generated by DNA sequences that were susceptible to DNA DSBs (55). These DSBs generate broken chromosomes that must then become stabilized by telomere healing or capture mechanisms to avoid potential BFB cycles. However, repetitive DNA sequence elements found at the end of a broken chromosome may also constitute a favorable site for stabilization by DNA repair mechanisms (54).

Low-Copy Repeats and Segmental Duplications

What generates the initial broken chromosome and why terminal deletions of 1p36 are ascertained so frequently is still unknown. This could reflect higher instability in this particular region of the genome or increased survival of terminal deletions of 1p36 over other telomeric abnormalities. Interestingly, one method uses an inverted duplication of the short arm (2). This was how McClintock originally formed a dicentric chromosome to generate broken chromosome sand initiate BFB cycles using a maize chromosome 9. A crossover between the normal homolog and the inverted portion of the duplicated chromosome, or between duplicated regions of sister chromatids, resulted in a dicentric chromosome that formed a bridge in anaphase with subsequent breakage (2). Large-scale sequence analysis of the terminal 10.5 Mb of 1p36 indicates that segmental duplications along with palindromic and inverted LCRs may be present in the distal subtelomeric regions (91). The region surrounding these LCRs forms a natural division between the interstitial deletion breakpoints of 1p36 and nearly all of the terminal deletion breakpoints (Ballif, Gajecka, and Shaffer, unpublished data). It is tempting to speculate that NAHR between palindromic or inverted LCRs in the subtelomeric region of 1p36 could be responsible for generating a dicentric chromosome that is broken at a random location during the subsequent anaphase as the centromeres move to opposite poles (Fig. 2).

Similar models have been proposed for generating inverted duplication/deficiency chromosomes, although those models were based on subtelomeric LCRs located in inverted orientations and positioned several megabases apart (92-94). The palindromic repeats proposed in this model for terminal deletions of 1p36 would provide a single site for NAHR with subsequent breakage of the newly formed dicentric chromosome generating variable-sized terminally deleted and inverted duplication/deficiency chromosomes. Stabilization of the broken chromosomes could then occur by a variety of DSB repair pathways (Fig. 1). Although duplication/deletion chromosomes would also be expected to occur, it is likely that these reciprocal products have not been ascertained in studies of monosomy 1p36 because they would be predicted to have much smaller imbalances and may present with a mild phenotype that is not typical of the syndrome.

Because the genomic sequence of 1p36 is not in its finished form, the precise size and orientation of these putative LCRs is still under investigation (91). However, regions of the genome that contain large duplications are notoriously difficult to map and sequence (68,95,96). A closer examination of the subtelomeric regions of all chromosomes may be useful for understanding the molecular basis of other terminally deleted chromosomes.

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