@article {1115,
	title = {Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation.},
	journal = {BMC genomics},
	volume = {16},
	year = {2015},
	month = {2015 Feb 13},
	pages = {69},
	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{\textquoteright} 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.},
	issn = {1471-2164},
	doi = {10.1186/s12864-015-1280-3},
	url = {http://www.biomedcentral.com/1471-2164/16/69},
	author = {Terol, Javier and Iba{\~n}ez, Victoria and Carbonell, Jos{\'e} and Alonso, Roberto and Estornell, Leandro H and Licciardello, Concetta and Gut, Ivo G and Joaqu{\'\i}n Dopazo and Talon, Manuel}
}
@article {563,
	title = {Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation},
	journal = {BMC Genomics},
	volume = {16},
	year = {2015},
	month = {Feb},
	pages = {69},
	abstract = {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.},
	issn = {1471-2164},
	doi = {10.1186/s12864-015-1280-3},
	url = {https://doi.org/10.1186/s12864-015-1280-3},
	author = {Terol, Javier and Iba{\~n}ez, Victoria and Carbonell, Jos{\'e} and Alonso, Roberto and Estornell, Leandro H. and Licciardello, Concetta and Gut, Ivo G. and Dopazo, Joaquin and Talon, Manuel}
}
@article {517,
	title = {Inferring the regulatory network behind a gene expression experiment.},
	journal = {Nucleic Acids Res},
	volume = {40},
	year = {2012},
	month = {2012 Jul},
	pages = {W168-72},
	abstract = {<p>Transcription factors (TFs) and miRNAs are the most important dynamic regulators in the control of gene expression in multicellular organisms. These regulatory elements play crucial roles in development, cell cycling and cell signaling, and they have also been associated with many diseases. The Regulatory Network Analysis Tool (RENATO) web server makes the exploration of regulatory networks easy, enabling a better understanding of functional modularity and network integrity under specific perturbations. RENATO is suitable for the analysis of the result of expression profiling experiments. The program analyses lists of genes and search for the regulators compatible with its activation or deactivation. Tests of single enrichment or gene set enrichment allow the selection of the subset of TFs or miRNAs significantly involved in the regulation of the query genes. RENATO also offers an interactive advanced graphical interface that allows exploring the regulatory network found.RENATO is available at: http://renato.bioinfo.cipf.es/.</p>},
	keywords = {Binding Sites, Databases, Genetic, Fanconi Anemia, Gene Regulatory Networks, Internet, MicroRNAs, Software, Transcription Factors, Transcriptome},
	issn = {1362-4962},
	doi = {10.1093/nar/gks573},
	author = {Bleda, Marta and Medina, Ignacio and Alonso, Roberto and De Maria, Alejandro and Salavert, Francisco and Dopazo, Joaquin}
}
