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BMC Genomics. 2015 Feb 13;16:69. doi: 10.1186/s12864-015-1280-3.

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

Author information

1
Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain. terol_javalc@gva.es.
2
Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain. ibanez_vic@gva.es.
3
Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain. jcarbonell.cipf@gmail.com.
4
Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain. ralonso@cipf.es.
5
Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain. lehues@hotmail.com.
6
CRA-ACM, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Corso Savoia 190, 95024, Acireale, Catania, Italy. concetta.licciardello@entecra.it.
7
Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028, Barcelona, Spain. igut@pcb.ub.cat.
8
Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain. jdopazo@cipf.es.
9
Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain. talon_man@gva.es.

Abstract

BACKGROUND:

Transposable-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.

RESULTS:

Based 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.

CONCLUSIONS:

Taken 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.

PMID:
25758634
PMCID:
PMC4334395
DOI:
10.1186/s12864-015-1280-3
[Indexed for MEDLINE]
Free PMC Article

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