Chromosomal Translocation Mechanisms at Intronic Alu Elements in Mammalian Cells

Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA.
Molecular Cell (Impact Factor: 14.02). 04/2005; 17(6):885-94. DOI: 10.1016/j.molcel.2005.02.028
Source: PubMed


Repetitive elements comprise nearly half of the human genome. Chromosomal rearrangements involving these elements occur in somatic and germline cells and are causative for many diseases. To begin to understand the molecular mechanisms leading to these rearrangements in mammalian cells, we developed an intron-based system to specifically induce chromosomal translocations at Alu elements, the most numerous family of repetitive elements in humans. With this system, we found that when double-strand breaks (DSBs) were introduced adjacent to identical Alu elements, translocations occurred at high frequency and predominantly arose from repair by the single-strand annealing (SSA) pathway (85%). With diverged Alu elements, translocation frequency was unaltered, yet pathway usage shifted such that nonhomologous end joining (NHEJ) predominated as the translocation pathway (93%). These results emphasize the fluidity of mammalian DSB repair pathway usage. The intron-based system is highly adaptable to addressing a number of issues regarding molecular mechanisms of genomic rearrangements in mammalian cells.

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Available from: Christine Richardson, Jan 22, 2015
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    • "2) The instability estimates derived from the I∶D ratio assumes no instability between direct oriented pairs. Several studies have shown that both inter-chromosomal and intra-chromosomal recombination occurs between Alu elements [5], [31], [34]. "
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    ABSTRACT: The human retrotransposon with the highest copy number is the Alu element. The human genome contains over one million Alu elements that collectively account for over ten percent of our DNA. Full-length Alu elements are randomly distributed throughout the genome in both forward and reverse orientations. However, full-length widely spaced Alu pairs having two Alus in the same (direct) orientation are statistically more prevalent than Alu pairs having two Alus in the opposite (inverted) orientation. The cause of this phenomenon is unknown. It has been hypothesized that this imbalance is the consequence of anomalous inverted Alu pair interactions. One proposed mechanism suggests that inverted Alu pairs can ectopically interact, exposing both ends of each Alu element making up the pair to a potential double-strand break, or "hit". This hypothesized "two-hit" (two double-strand breaks) potential per Alu element was used to develop a model for comparing the relative instabilities of human genes. The model incorporates both 1) the two-hit double-strand break potential of Alu elements and 2) the probability of exon-damaging deletions extending from these double-strand breaks. This model was used to compare the relative instabilities of 50 deletion-prone cancer genes and 50 randomly selected genes from the human genome. The output of the Alu element-based genomic instability model developed here is shown to coincide with the observed instability of deletion-prone cancer genes. The 50 cancer genes are collectively estimated to be 58% more unstable than the randomly chosen genes using this model. Seven of the deletion-prone cancer genes, ATM, BRCA1, FANCA, FANCD2, MSH2, NCOR1 and PBRM1, were among the most unstable 10% of the 100 genes analyzed. This algorithm may lay the foundation for comparing genetic risks posed by structural variations that are unique to specific individuals, families and people groups.
    Full-text · Article · Jun 2013 · PLoS ONE
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    • "However, the presence of an Alu sequence itself is not sufficient. It is more the nature of this sequence that induces double-strand breaks and provides an initiation point for recombination [106] [107]. Although rare in somatic cells, the existence of ectopic recombination between Alu sequences leads to DNA deletions in germ cells (Table 1) [107]. "
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    ABSTRACT: Transposable elements are present in almost all genomes including that of humans. These mobile DNA sequences are capable of invading genomes and their impact on genome evolution is substantial as they contribute to the genetic diversity of organisms. The mobility of transposable elements can cause deleterious mutations, gene disruption and chromosome rearrangements that may lead to several pathologies including cancer. This mini-review aims to give a brief overview of the relationship that transposons and retrotransposons may have in the genetic cause of human cancer onset, or conversely creating protection against cancer. Finally, the cause of TE mobility may also be the cancer cell environment itself.
    Full-text · Article · Sep 2012 · Biochimica et Biophysica Acta
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    • "Only non-crossover products are formed by SDSA. SSA (Figure 2D) allows rapid repair of breaks within tandem repeat arrays, for example at the yeast and mammalian ribosomal DNA loci (Liang et al., 1998; Elliott et al., 2005; Fishman-Lobell et al., 1992; Liefshitz et al., 1995; Park et al., 1999). SSA initiates at resected DSB ends, but unlike other types of homologous recombination, it is intrachromosomal; it does not involve strand invasion and does not require a homologous chromosome or sister chromatid. "
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    ABSTRACT: Repetitive DNA is present in the eukaryotic genome in the form of segmental duplications, tandem and interspersed repeats, and satellites. Repetitive sequences can be beneficial by serving specific cellular functions (e.g. centromeric and telomeric DNA) and by providing a rapid means for adaptive evolution. However, such elements are also substrates for deleterious chromosomal rearrangements that affect fitness and promote human disease. Recent studies analyzing the role of nuclear organization in DNA repair and factors that suppress non-allelic homologous recombination (NAHR) have provided insights into how genome stability is maintained in eukaryotes. In this review, we outline the types of repetitive sequences seen in eukaryotic genomes and how recombination mechanisms are regulated at the DNA sequence, cell organization, chromatin structure, and cell cycle control levels to prevent chromosomal rearrangements involving these sequences.
    Full-text · Article · Apr 2012 · Critical Reviews in Biochemistry and Molecular Biology
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