Environmental and epigenetic regulation of Rider retrotransposons in tomato
First author: Matthias Benoit; Affiliations: University of Cambridge (剑桥大学): Cambridge, UK
Corresponding author: Matthias Benoit
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.
作物中的转座元件是表型变异的有力驱动者，在驯化和育种项目中受到了广泛的选择。在番茄中，长末端重复逆转座子家族Rider的转位已经作用于多个农艺性状的表型，比如果实形状和颜色。然而，调控Rider活性的分子机制还不清楚。本文中，作者开发了一套生物信息流程用于对包含LTR在内的逆转座子的功能鉴定，并且鉴定了番茄基因组中所有Rider元件的全长。随后，作者的研究显示Rider转录本和以染色体外DNA形式存在的转位中间体的积累由干旱胁迫所诱导，并且依赖于脱落酸ABA的信号。作者进一步的研究证明了Rider的残基活性受到表观机制的调控，这些表观机制涉及了siRNA和RNA依赖性的DNA甲基化途径。最终，作者发现在其他植物物种中广泛存在类似于Rider的转座元件。本文的研究鉴定了Rider是一个环境响应型转座元件，对于植物来说是一个潜在的遗传和表观变异来源。
通讯：Matthias Benoit (https://www.cshl.edu/research/postdoctoral-research/postdocs/matthias-benoit/)
个人简介：2008年，苏格兰罗伯特戈登大学，学士；2009-2010年，法国保罗萨巴蒂埃大学，硕士；2014年，法国布莱斯·帕斯卡大学，博士；2015-2018年，英国剑桥大学，博士后；2019-至今，美国冷泉港实验室，博士后。
研究方向：在番茄发育、驯化和育种过程中的基因组和表观遗传变异。
doi: https://doi.org/10.1371/journal.pgen.1008370
Journal: PLOS Genetics
Published online: September 16, 2019
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