Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity

Abstract

The ubiquity of mobile elements in mammalian genomes poses considerable challenges for the maintenance of genome integrity. The predisposition of mobile elements towards participation in genomic rearrangements is largely a consequence of their interspersed homologous nature. As tracts of nonallelic sequence homology, they have the potential to interact in a disruptive manner during both meiotic recombination and DNA repair processes, resulting in genomic alterations ranging from deletions and duplications to large-scale chromosomal rearrangements. Although the deleterious effects of transposable element (TE) insertion events have been extensively documented, it is arguably through post-insertion genomic instability that they pose the greatest hazard to their host genomes. Despite the periodic generation of important evolutionary innovations, genomic alterations involving TE sequences are far more frequently neutral or deleterious in nature. The potentially negative consequences of this instability are perhaps best illustrated by the >25 human genetic diseases that are attributable to TE-mediated rearrangements. Some of these rearrangements, such as those involving the MLL locus in leukemia and the LDL receptor in familial hypercholesterolemia, represent recurrent mutations that have independently arisen multiple times in human populations. While TE-instability has been a potent force in shaping eukaryotic genomes and a significant source of genetic disease, much concerning the mechanisms governing the frequency and variety of these events remains to be clarified. Here we survey the current state of knowledge regarding the mechanisms underlying mobile element-based genetic instability in mammals. Compared to simpler eukaryotic systems, mammalian cells appear to have several modifications to their DNA-repair ensemble that allow them to better cope with the large amount of interspersed homology that has been generated by TEs. In addition to the disruptive potential of nonallelic sequence homology, we also consider recent evidence suggesting that the endonuclease products of TEs may also play a key role in instigating mammalian genomic instability.

Figure 1. Classic Double-strand Break Repair (DBSR) Model

In the classic model for recombination-mediated DSB repair, invasion of the undamaged template by the exposed 3' ends of both sides of the break junction (indicated by yellow arrows), primes the synthesis of the nascent DNA used for repair and forms a pair of holiday junctions. As indicated in the lower portion of the figure, depending on how these Holiday junctions are resolved, the DBSR model predicts crossover and noncrossover (“gene conversion”) events will occur with approximately equal frequency.

Figure 2. Nonallelic Homologous Recombination Events Among TEs Generate Multiple Rearrangments

Three of several possible rearrangments resulting from nonallelic recombination are depicted. In the first instance, misallignment of sister chromatids during recombination or DNA repair yield insertion and deletion mutations. In the second instance, recombination between two homolgous TEs in direct orientation on the same physical chromsome results in an inversion of the intervening sequence. In the third image, alignment with a nonhomologous chromosome results in the translocation of chromosome arms.

Figure 3. Three Variations of Synthesis-Dependent Strand Annealing (SDSA)

a) invasion of the undamaged template chromosome simultaneously by both 3' strands (indicated by yellow arrows) of the broken chromosome primes the synthesis of new DNA. Unlike the DBSR model, however, the newly synthesized strands anneal together and result in no crossover. b) In this model, only one strand invades the target template. Following synthesis, the new DNA strand reattaches to the originally damaged chromosome at a homologous location, resulting in a gene conversion repair without crossover. c) In this scenario, the DSB occurs adjacent to a TE insertion. The 3' end of the broken DNA strand invades the template strand at a nonallelic yet homologous TE locus. Synthesis occurs, copying both the homologous TE locus as well as the nonhomologous sequence flanking it. NHEJ is then used to reunite the newly synthesized sequence to the original damaged chromosome.

Figure 4. Single Strand Annealing (SSA)

In the SSA model, the 5' ends surrounding the breakage region are “chewed back” or resected, exposing adjacent homology. The homologous strands anneal with each other and are ligated, resulted in the deletion of intervening sequence.

Figure 5. Enonuclease Target Site Duplications (TSDs) Adjacent to SINEs and LINEs Invite DSB Instability

Insertion of SINEs and LINEs by the TPRT mechanism results in the duplication of the pre-insertion endonuclease cleavage site. The persistance of these sights adjacent to the element allows for subsequent cleavage by other L1 endonucleases. The DSBs generated by these L1 endonucleases, coupled with the adjacency of the TSDs to sequences with interspersed homologous copies, gives them a high potential for generating rearrangement events. Orange arrows indicate endonuclease target sites, which are part of the TSDs following TE insertion. Purple shapes represent L1 endonuclease molecules.