Abstract
Nature has found many ways to utilize transposable elements (TEs) throughout evolution. Many molecular and cellular processes depend on DNA-binding proteins recognizing hundreds or thousands of similar DNA motifs dispersed throughout the genome that are often provided by TEs. It has been suggested that TEs play an important role in the evolution of such systems, in particular, the rewiring of gene regulatory networks. One mechanism that can further enhance the rewiring of regulatory networks is nonallelic gene conversion between copies of TEs. Here, we will first review evidence for nonallelic gene conversion in TEs. Then, we will illustrate the benefits nonallelic gene conversion provides in rewiring regulatory networks. For instance, nonallelic gene conversion between TE copies offers an alternative mechanism to spread beneficial mutations that improve the network, it allows multiple mutations to be combined and transferred together, and it allows natural selection to work efficiently in spreading beneficial mutations and removing disadvantageous mutations. Future studies examining the role of nonallelic gene conversion in the evolution of TEs should help us to better understand how TEs have contributed to evolution.
Highlights
Eukaryotic genomes contain many DNA-binding proteins which bind to thousands of sites in the genome sharing a common DNA motif
Deleterious mutations can be reverted to its original state by gene conversion. Another important advantage is that selection can work much more efficiently to spread beneficial mutations and eliminate deleterious mutations when nonallelic gene conversion is occurring between the different copies, which has been demonstrated for multigene families (Mano and Innan 2008)
We described the impact of nonallelic gene conversion between transposable elements (TEs) copies above in the context of the rewiring of networks, the same discussion should apply to the evolution of TE families in general
Summary
Eukaryotic genomes contain many DNA-binding proteins which bind to thousands of sites in the genome sharing a common DNA motif. Some motifs are $10 bp whereas others, such as the CTCF-binding motif (Schmidt et al 2012), are as long as $30 bp and most motifs allow a certain amount of mismatches How these networks can evolve has been of great interest because 1) the coevolution involving the DNA-binding protein and so many different motifs should be extremely difficult by independent mutations, and 2) the creation of such a large number of new motifs by independent mutations should not be so easy either. Evol. 11(7):1723–1729. doi:10.1093/gbe/evz124 Advance Access publication June 18, 2019
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