L1 recombination-associated deletions generate human genomic variation

Abstract

Mobile elements have created structural variation in the human genome through their de novo insertions and post-insertional genomic rearrangements. L1 elements are a type of long interspersed element (LINE) that is dispersed at high copy numbers within most mammalian genomes. To determine the magnitude of L1 recombination-associated deletions (L1RADs), we computationally extracted L1RAD candidates by comparing the human and chimpanzee genomes and verified each of the L1RAD events by using wet-bench analyses. Through these analyses, we identified 73 human-specific L1RAD events that occurred subsequent to the divergence of the human and chimpanzee lineages. Despite their low frequency, the L1RAD events deleted Ϸ450 kb of the human genome. One L1RAD event generated a large deletion of Ϸ64 kb. Multiple alignments of prerecombination and postrecombination L1 elements suggested that two different deletion mechanisms generated the L1RADs: nonallelic homologous recombination (55 events) and nonhomologous end joining between two L1s (18 events). In addition, the position of L1RADs throughout the genome does not correlate with local chromosomal recombination rates. This process may be implicated in the partial regulation of L1 copy numbers by the finding that Ϸ60% of the DNA sequences deleted by the L1RADs consist of L1 sequences that were either directly involved in the recombination events or located in the intervening sequence between recombining L1s. Overall, there is increasing evidence that L1RADs have played an important role in creating structural variation.LINE-1 ͉ nonallelic homologous ͉ nonhomologous end joining ͉ retrotransposon L ong interspersed elements (LINE-1s or L1s) are universal constituents of mammalian genomes and account for Ϸ17% of the human genome (1). They have expanded to Ϸ 520,000 copies over the last 150 million years (1, 2). Full-length L1s are Ϸ6 kb long, and encode two ORFs (ORF1 and ORF2), which code for a 40-kDa RNA-binding protein with nucleic acid chaperone activity (3) and a 150-kDa protein with both endonuclease (EN) and reverse transcriptase (RT) activities (4-6). L1s mobilize via an RNA intermediate to integrate themselves into genomic DNA at the target site. However, Ϸ99.8% of L1s in the human genome are unable to retrotranspose (7), either because of point mutations or structural deficiencies (e.g., 5Ј truncations, 5Ј inversions, or other internal rearrangements) (8 -10). Consequently, only 80 -100 retrotranspositioncompetent L1s capable of autonomous retrotransposition are located in the human genome (7,11).Homologous recombination between closely related DNA fragments occurs in all living organisms (12, 13). A recent study of human genomic deletions caused by unequal homologous recombination between two Alu elements showed that 492 human-specific deletion events resulted in a total of Ϸ400 kb DNA being lost since the divergence of the human and chimpanzee lineages (14). Similar to the Alu elements, L1s may have been a source of recombination-associated genomic deletion throughou...

Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control

“…They can generate structural variation through insertion-mediated deletion, in which the insertion of an L1 element can result in the deletion of the adjacent genomic sequence (Symer et al 2002;Gilbert et al 2002Gilbert et al , 2005 and via nonallelic homologous recombination between L1s that can create insertions, deletions, and inversions (Han et al 2008;Cordaux and Batzer 2009). Active L1s have been shown to be a major source of variation within the human population (Beck et al 2010;Huang et al 2010;Iskow et al 2010) and can modulate gene expression, for example, by alternative splicing (Belancio et al 2006), disrupting transcription (Han et al 2004), and generating alternative promoters (Speek 2001).…”

The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important

“…Transposable elements (TEs), once labeled as ''junk'' DNA, contribute to unprecedented levels of interspecific divergence (Lander et al 2001; The Chimpanzee Sequencing and Analysis Consortium 2005; Han et al 2007; Rhesus Macaque Genome Sequencing and Analysis Consortium 2007), intraspecific genome diversity (Batzer and Deininger 2002;Bennett et al 2004;Seleme et al 2006;Han et al 2008), and human diseases such as hemophilias A and B, as well as common cancers (Batzer and Deininger 2002;Chen et al 2005). Recently, the intra-and interchromosomal distributions of short and long interspersed nuclear elements (SINEs and LINEs, respectively), the most abundant classes of TEs in primate genomes (Rhesus Macaque Genome Sequencing and Analysis Consortium 2007), have received critical attention.…”

Homozygous deletion of DIS3L2 exon 9 due to non-allelic homologous recombination between LINE-1s in a Japanese patient with Perlman syndrome

“…The similarity between L1-A and L1-B was high (99.0%), and the interval was shorter than that of the human lineage-specific L1 recombination-associated deletion (B450 kb). 16 These conditions might enable the L1-mediated NAHR to cause disease, although the possibility of microhomology-mediated replication-dependent recombination models, such as fork stalling and template switching, microhomology-mediated break-induced replication and serial replication slippage, could not be ruled out. 17 The deletion size of exon 9 in the patients reported by Astuti et al 2 , found in two Dutch pedigrees and one cell line established from a Caucasian patient, strongly suggests the same mechanism at work, although this was not mentioned.…”