Comparative Studies Evolutionary Origins of NAHR Hotspots

The likely dependence of NAHR rates on levels of sequence similarity between paralogs suggests that monitoring the evolution of this similarity may inform our understanding of the time-depth of NAHR hotspots. One recent study of NAHR between paralogous human endogenous retrovirus (HERV) proviral sequences, flanking the Y-chromosome Azoospermia Factor a (AZFa) locus that when deleted causes male infertility, provided evidence for several hominid-specific gene conversion events that may have rendered the associated hotspots better substrates for chromosomal rearrangements in humans than in either chimpanzees or gorillas (41). Gene conversion generates signatures of concerted evolution in alignments of comparative sequences (see Fig. 3) and in the AZFa-HERVs these signatures are coincident with the location of the NAHR hotspots. If we continue the "premutation" analogy, homogenizing permutations have occurred on the hominid lineage and become fixed in an ancestral species to modern humans. However, because gene conversion and chromosomal rearrangement reflect the alternative products of a common intermediate, it may be that a recombinogenic sequence motif/structure underpins the association and the increased sequence identity resulting from gene conversion plays only a minor role in determining the frequency of chromosomal rearrangement. Nevertheless, the coincidence of signatures of concerted evolution and recurrent breakpoints of chromosomal rearrangements (mapped at the DNA sequence level) may enable the identification of putative rearrangement hotspots from analysis of comparative sequences from great apes.

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