Recent researches have argued that truncated LTR elements were mainly caused by unequal homologous or illegitimate recombination within genome and the result of recombination was the deletion of genomic sequences [ 27, 32, 35, 36].
For example, it was estimated that ~200 Mb of LTR-retrotransposon DNA was removed from the rice genome by unequal homologous recombination and illegitimate recombination within the past 5 million years [ 9, 10], although neither amplification nor removal of LTR-retrotransposons seems to be absolutely gradual processes [ 14].
Another possibility is that a DSB, locally associated with other types of DNA damage, for example, abasic sites (Sutherland et al, 2000) could cause error-proneness of topoisomerase II α, causing illegitimate rearrangements within a damaged chromatin domain of a radiation-exposed cell.
If the positive reviews were all published within 48 hours of each other, it's most likely the company hired people to submit fake, illegitimate reviews within a certain deadline.
The UTR~LTR junction may have formed via intrastrand illegitimate recombination events within a single (as illustrated in Figure 3) or between nested elements.
This could facilitate the occurrence of illegitimate recombination events within the LMW-GS genes and result in novel allelic variations, such as chimeric genes [ 9].
Reverse transcriptase PCR (RT-PCR) analysis revealed that MO-4 treatment induced a mis-splicing event using an illegitimate splice site within exon 1B, resulting in the production of an anomalous isoform lacking the 3′ 42 bp of the exon, as shown in supplementary material Fig. S3.
Therefore, it would be conceivable that besides layered retroelements other sequences could insert within retroelements by illegitimate recombination.
It contains nucleosomes whose histones are deacetylated by Sir2 protein, which suppresses illegitimate recombination between different units within the array and so prevents collapse of the array (Kobayashi et al. 2004).
By contrast, when sequences are not only evolving in a tree-like fashion, i.e. when segments of divergent sequences fuse to form a single a gene, or when segments within genes recombine through illegitimate recombination, sequences are connected by edges that are not necessarily "full homology" edges [ 23].
