Characterization of pre-insertion loci of de novo L1 insertions

Abstract

The human Long Interspersed Element-1 (LINE-1) and the Short Interspersed Element (SINE) Alu comprise 28% of the human genome. They share the same L1-encoded endonuclease for insertion, which recognizes an A+T-rich sequence. Under a simple model of insertion distribution, this nucleotide preference would lead to the prediction that the populations of both elements would be biased towards A+T-rich regions. Genomic L1 elements do show an A+T-rich bias. In contrast, Alu is biased towards G+C-rich regions when compared to the genome average. Several analyses have demonstrated that relatively recent insertions of both elements show less G+C content bias relative to older elements. We have analyzed the repetitive element and G+C composition of more than 100 pre-insertion loci derived from de novo L1 insertions in cultured human cancer cells, which should represent an evolutionarily unbiased set of insertions. An A+T-rich bias is observed in the 50 bp flanking the endonuclease target site, consistent with the known target site for the L1 endonuclease. The L1, Alu, and G+C content of 20 kb of the de novo pre-insertion loci show a different set of biases than those observed for fixed L1s in the human genome. In contrast to the insertion sites of genomic L1s, the de novo L1 pre-insertion loci are relatively L1-poor, Alu-rich and G+C-neutral. Finally, a statistically significant cluster of de novo L1 insertions was localized in the vicinity of the c-myc gene. These results suggest that the initial insertion preference of L1, while A+T-rich in the initial vicinity of the break site, can be influenced by the broader content of the flanking genomic region and have implications for understanding the dynamics of L1 and Alu distributions in the human genome.

Heritable L1 retrotransposition in the mouse primordial germline and early embryo

“…S1E, S4;Singer et al 1983;Scott et al 1987;Luan et al 1993;Moran et al 1996;Jurka 1997). The average GC content of de novo L1 insertion sites within a 50-bp and 20-kb window of the endonuclease cleavage position was 30% and 38%, respectively, consistent with a previously described preference of L1 for AT-rich regions (Supplemental Table 4; Szak et al 2002;Boissinot et al 2004;Gasior et al 2007). One insertion (insertion #5) (Fig.…”

Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health

“…As a result of unequal selective pressures across the genome, the patterns of element distribution observed via genome sequencing will not necessarily coincide with the initial pattern of insertions. For example, although L1 elements in humans are generally found in gene-poor AT-rich regions, data from cell culture suggest that this may be an effect of post-insertional processes rather than an initial insertion preference dictated by L1 biology (Ovchinnikov et al 2001;Graham and Boissinot 2006;Gasior et al 2007). Similar results were obtained when L1 integration events were characterized in transgenic animals Babushok et al 2006), suggesting that the discrepancy in the distribution between new and old L1 integration events is likely to arise from post-insertional selection pressures.…”

“…L1 elements are present at a higher density on the X chromosome than any other chromosome (Lander et al 2001), and it remains possible that some of this density increase may represent insertion preference. However, there was no detectable enrichment of L1 element insertions on the X chromosome in tissue culture studies that directly measures de novo L1 insertions (Graham and Boissinot 2006;Gasior et al 2007), and the enrichment on the X chromosome has largely been ascribed to lower recombination rates and corresponding reduction in the efficiency of negative selection among the sex chromosomes (Boissinot et al 2001). In contrast, 31 endogenous retroviral insertions in mice (Ostertag and Kazazian 2001a;Maksakova et al 2006) have been detected, and none of those insertions was found to reside on the X chromosome.…”

Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition

“…3A). L1s are also enriched in A/T-rich genomic regions (Gasior et al 2007). Variation in L1 polymorphism densities along chromosomes is not due simply to differences in WGS trace coverage (Supplemental Fig.…”