Environmental and epigenetic regulation of Rider retrotransposons in tomato

Autoři: Matthias Benoit aff001;  Hajk-Georg Drost aff001;  Marco Catoni aff001;  Quentin Gouil aff002;  Sara Lopez-Gomollon aff002;  David Baulcombe aff002;  Jerzy Paszkowski aff001
Působiště autorů: The Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom aff001;  Department of Plant Sciences, University of Cambridge, Cambridg, United Kingdom aff002
Vyšlo v časopise: Environmental and epigenetic regulation of Rider retrotransposons in tomato. PLoS Genet 15(9): e1008370. doi:10.1371/journal.pgen.1008370
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008370


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.

Klíčová slova:

Biology and life sciences – Organisms – Eukaryota – Plants – Fruits – Tomatoes – Solanum – Genetics – Gene expression – Gene regulation – Small interfering RNAs – Epigenetics – DNA modification – DNA – Genetic elements – Retrotransposons – Genomics – Mobile genetic elements – Transposable elements – Plant genomics – Plant genetics – Biochemistry – Nucleic acids – RNA – Non-coding RNA – Cell biology – Chromosome biology – Chromatin – Chromatin modification – DNA methylation – Bioengineering – Biotechnology – Plant biotechnology – Plant science – Research and analysis methods – Database and informatics methods – Bioinformatics – Sequence analysis – Sequence motif analysis – Sequence alignment – Engineering and technology


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