Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation.

Victoria Ibañez,Joaquín Dopazo,Roberto Alonso,Ivo G Gut,Leandro H Estornell,Manuel Talon,Javier Terol,José Carbonell,Concetta Licciardello

doi:10.1186/s12864-015-1280-3

Abstract

BackgroundTransposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major factor contributing to rearrangements. However, the whole issue of DSB proximity remains virtually unexplored.ResultsBased on DNA sequencing analysis we show that the genomes of 2 derived mutations, Arrufatina (sport) and Nero (irradiation), share a similar 2 Mb deletion of chromosome 3. A 7 kb Mutator-like element found in Clemenules was present in Arrufatina in inverted orientation flanking the 5′ end of the deletion. The Arrufatina Mule displayed “dissimilar” 9-bp target site duplications separated by 2 Mb. Fine-scale single nucleotide variant analyses of the deleted fragments identified a TTC-repeat sequence motif located in the center of the deletion responsible of a meiotic crossover detected in the citrus reference genome.ConclusionsTaken together, this information is compatible with the proposal that in both mutants, the TTC-repeat motif formed a triplex DNA structure generating a loop that brought in close proximity the originally distinct reactive ends. In Arrufatina, the loop brought the Mule ends nearby the 2 distinct insertion target sites and the inverted insertion of the transposable element between these target sites provoked the release of the in-between fragment. This proposal requires the involvement of a unique transposon and sheds light on the unresolved question of how two distinct sites become located in close proximity. These observations confer a crucial role to the TTC-repeats in fundamental plant processes as meiotic recombination and chromosomal rearrangements.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1280-3) contains supplementary material, which is available to authorized users.

Highlights

Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity
In the current work we provide evidence in citrus suggesting that a TTC-repeat motif of a meiotic crossover hot spot might enable the proximity of two distant sequences facilitating transposition of a transposable elements (TEs) that as a consequence generated a gross deletion
Aside from the identification of Mules in citrus and the first report on the conspicuous accumulation of several motifs involved in human chromosome breaks in a TE end terminus, this work highlights overall two major findings: the identification of a TTC-repeat as a motif physically responsible of meiotic recombination in plants and its involvement in the generation of gross deletions

Summary

Introduction

Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. DSB proximity is a major factor contributing to rearrangements. One of the major lines of evidence supporting that structural variations in genomes have a strong impact on phenotypic diversity comes from the study of human genomes (www.1000genomes.org/) and their prevalence on diseases [1]. It is well known that structural genome variations may occur through numerous processes, i.e. segmental duplications, illegitimate recombination or transposable elements (TEs) activity [1,2]. “Clemenules”, (CLE) a collection of induced mutants in order to increase phenotypic diversity. Since ionizing radiation is generally expected to produce mostly deletions [6] it was hypothesized that a similar deletion

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