Environmental and epigenetic regulation of Rider retrotransposons in tomato

Benoit, M., Drost, H. G., Catoni, M., Gouil, Q., Lopez-Gomollon, S., Baulcombe, D., Paszkowski, J. (September 2019) Environmental and epigenetic regulation of Rider retrotransposons in tomato. PLoS Genet, 15 (9). e1008370. ISSN 1553-7390

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Abstract

Transposable elements in crop plants are the powerful drivers of phenotypic variation that has been selected during domestication and breeding programs. In tomato, transpositions of the LTR (long terminal repeat) retrotransposon family Rider have contributed to various phenotypes of agronomical interest, such as fruit shape and colour. However, the mechanisms regulating Rider activity are largely unknown. We have developed a bioinformatics pipeline for the functional annotation of retrotransposons containing LTRs and defined all full-length Rider elements in the tomato genome. Subsequently, we showed that accumulation of Rider transcripts and transposition intermediates in the form of extrachromosomal DNA is triggered by drought stress and relies on abscisic acid signalling. We provide evidence that residual activity of Rider is controlled by epigenetic mechanisms involving siRNAs and the RNA-dependent DNA methylation pathway. Finally, we demonstrate the broad distribution of Rider-like elements in other plant species, including crops. Our work identifies Rider as an environment-responsive element and a potential source of genetic and epigenetic variation in plants.

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation bioinformatics > genomics and proteomics > genetics & nucleic acid processing > epigenetics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > epigenetics organism description > plant > tomato bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > transposable elements
CSHL Authors:	Benoit, Matthias
Communities:	CSHL labs > Lippman lab
Depositing User:	Matthew Dunn
Date:	16 September 2019
Date Deposited:	08 Nov 2019 19:28
Last Modified:	08 Nov 2019 19:28
PMCID:	PMC6762207
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/38647

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