Abstract
Transposable elements (TEs) allow rewiring of regulatory networks, and the recent amplification of the ISX element dispersed 77 functional but suboptimal binding sites for the dosage compensation complex to a newly formed X chromosome in Drosophila. Here we identify two linked refining mutations within ISX that interact epistatically to increase binding affinity to the dosage compensation complex. Selection has increased the frequency of this derived haplotype in the population, which is fixed at 30% of ISX insertions and polymorphic among another 41%. Sharing of this haplotype indicates that high levels of gene conversion among ISX elements allow them to 'crowd-source' refining mutations, and a refining mutation that occurs at any single ISX element can spread in two dimensions: horizontally across insertion sites by non-allelic gene conversion, and vertically through the population by natural selection. These results describe a novel route by which fully functional regulatory elements can arise rapidly from TEs and implicate non-allelic gene conversion as having an important role in accelerating the evolutionary fine-tuning of regulatory networks.
Highlights
A substantial portion of animal genomes is composed of repetitive sequences, including gene duplicates, satellite DNA, and transposable elements
To identify potential refining mutations that optimize MSL-binding at chromatin entry sites derived from the ISX element, we characterized sequence variation within the MSL recognition motifs and flanking sequence regions for all 77 insertions of the ISX element on the neo-X chromosome in the sequenced reference strain MSH22 (Figure 1A)
Because we have previously demonstrated that ISX contains a functional MSL recognition motif but the closely related ISY element does not (Ellison and Bachtrog, 2013), we sought to identify sequence variants that were present in multiple ISX elements but rare or absent in ISY elements from the same chromosome
Summary
A substantial portion of animal genomes is composed of repetitive sequences, including gene duplicates, satellite DNA, and transposable elements. Compared to single-copy genes, a family of gene duplicates presents a larger mutational target, and a mutation arising in any gene copy can be spread among copies by non-allelic gene conversion, thereby increasing the efficiency of both positive and purifying selection (Mano and Innan, 2008). Unlike regulatory elements where short binding motifs (10 basepairs on average for transcription factors; Stewart et al, 2012) evolve de novo via point mutation or microsatellite expansion, binding sites that evolve from TEs are initially almost identical in sequence and are nested within a larger repeat unit (hundreds or thousands of basepairs in size), and may be subject to non-allelic gene conversion.
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