Author response: Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements

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.

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Multiple Heterologies Increase Mitotic Double-Strand Break-Induced Allelic Gene Conversion Tract Lengths in Yeast

Genetics ◽

10.1093/genetics/153.2.665 ◽

1999 ◽

Vol 153 (2) ◽

pp. 665-679 ◽

Cited By ~ 3

Author(s):

Jac A Nickoloff ◽

Douglas B Sweetser ◽

Jennifer A Clikeman ◽

Guru Jot Khalsa ◽

Sarah L Wheeler

Keyword(s):

Gene Conversion ◽

Mismatch Repair ◽

Frameshift Mutation ◽

Strand Break ◽

Double Strand Break ◽

Chromosome Loss ◽

Allelic Gene ◽

Break Induced Replication ◽

Gene Conversion Tract ◽

Conversion Tract

Abstract Spontaneous and double-strand break (DSB)-induced allelic recombination in yeast was investigated in crosses between ura3 heteroalleles inactivated by an HO site and a +1 frameshift mutation, with flanking markers defining a 3.4-kbp interval. In some crosses, nine additional phenotypically silent RFLP mutations were present at ∼100-bp intervals. Increasing heterology from 0.2 to 1% in this interval reduced spontaneous, but not DSB-induced, recombination. For DSB-induced events, 75% were continuous tract gene conversions without a crossover in this interval; discontinuous tracts and conversions associated with a crossover each comprised ∼7% of events, and 10% also converted markers in unbroken alleles. Loss of heterozygosity was seen for all markers centromere distal to the HO site in 50% of products; such loss could reflect gene conversion, break-induced replication, chromosome loss, or G2 crossovers. Using telomere-marked strains we determined that nearly all allelic DSB repair occurs by gene conversion. We further show that most allelic conversion results from mismatch repair of heteroduplex DNA. Interestingly, markers shared between the sparsely and densely marked interval converted at higher rates in the densely marked interval. Thus, the extra markers increased gene conversion tract lengths, which may reflect mismatch repair-induced recombination, or a shift from restoration- to conversion-type repair.

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Evidence of extensive non-allelic gene conversion among LTR elements in the human genome

Scientific Reports ◽

10.1038/srep28710 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 19

Author(s):

Beniamino Trombetta ◽

Gloria Fantini ◽

Eugenia D’Atanasio ◽

Daniele Sellitto ◽

Fulvio Cruciani

Keyword(s):

Human Genome ◽

Gene Conversion ◽

Allelic Gene

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Eco-evolutionary dynamics

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0027 ◽

2009 ◽

Vol 364 (1523) ◽

pp. 1483-1489 ◽

Cited By ~ 339

Author(s):

F. Pelletier ◽

D. Garant ◽

A.P. Hendry

Keyword(s):

Time Scale ◽

Evolutionary Dynamics ◽

Evolutionary Change ◽

Ecological Change ◽

Evolutionary Changes ◽

Microevolutionary Change ◽

Theoretical Developments ◽

Rapid Evolutionary Change

Evolutionary ecologists and population biologists have recently considered that ecological and evolutionary changes are intimately linked and can occur on the same time-scale. Recent theoretical developments have shown how the feedback between ecological and evolutionary dynamics can be linked, and there are now empirical demonstrations showing that ecological change can lead to rapid evolutionary change. We also have evidence that microevolutionary change can leave an ecological signature. We are at a stage where the integration of ecology and evolution is a necessary step towards major advances in our understanding of the processes that shape and maintain biodiversity. This special feature about ‘eco-evolutionary dynamics’ brings together biologists from empirical and theoretical backgrounds to bridge the gap between ecology and evolution and provide a series of contributions aimed at quantifying the interactions between these fundamental processes.

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Meiotic recombination between repeated transposable elements in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.8.7.2942-2954.1988 ◽

1988 ◽

Vol 8 (7) ◽

pp. 2942-2954

Author(s):

M Kupiec ◽

T D Petes

Keyword(s):

Saccharomyces Cerevisiae ◽

Transposable Elements ◽

Gene Conversion ◽

Meiotic Recombination ◽

Small Region ◽

Ty Elements ◽

Ty Element ◽

Reciprocal Exchange ◽

Gene Conversions ◽

Conversion Tract

We have measured the frequency of meiotic recombination between marked Ty elements in the Saccharomyces cerevisiae genome. These recombination events were usually nonreciprocal (gene conversions) and sometimes involved nonhomologous chromosomes. The frequency of ectopic gene conversion among Ty elements appeared lower than expected on the basis of previous studies of recombination between artificially constructed repeats. The conversion events involved either a subset of the total Ty elements in the genome or the conversion tract was restricted to a small region of the Ty element. In addition, the observed conversion events were very infrequently associated with reciprocal exchange.

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