Downregulation of RdDM during strawberry fruit ripening

First author: Jingfei Cheng; Affiliations: CAS Center of Excellence in Molecular Plant Sciences (中国科学院分子植物科学卓越创新中心): Shanghai, China

Corresponding author: Zhaobo Lang

Recently, DNA methylation was proposed to regulate fleshy fruit ripening. Fleshy fruits can be distinguished by their ripening process as climacteric fruits, such as tomatoes, or non-climacteric fruits, such as strawberries. Tomatoes undergo a global decrease in DNA methylation during ripening, due to increased expression of a DNA demethylase gene. The dynamics and biological relevance of DNA methylation during the ripening of non-climacteric fruits are unknown. Here, we generate single-base resolution maps of the DNA methylome in immature (不成熟的) and ripe strawberry. We observe an overall loss of DNA methylation during strawberry fruit ripening. Thus, ripening-induced DNA hypomethylation occurs not only in climacteric fruit, but also in non-climacteric fruit. Application of a DNA methylation inhibitor causes an early ripening phenotype, suggesting that DNA hypomethylation is important for strawberry fruit ripening. The mechanisms underlying DNA hypomethylation during the ripening of tomato and strawberry are distinct. Unlike in tomatoes, DNA demethylase genes are not upregulated during the ripening of strawberries. Instead, genes involved in RNA-directed DNA methylation are downregulated during strawberry ripening. Further, ripening-induced DNA hypomethylation is associated with decreased siRNA levels, consistent with reduced RdDM activity. Therefore, we propose that a downregulation of RdDM contributes to DNA hypomethylation during strawberry ripening. Our findings provide new insight into the DNA methylation dynamics during the ripening of non-climacteric fruit and suggest a novel function of RdDM in regulating an important process in plant development.

最近，有研究显示DNA甲基化能够调控肉质果的成熟过程。肉质果根据成熟的过程可以分为番茄等跃变型果实和草莓等非跃变型果实。番茄在果实成熟过程中DNA去甲基化酶基因表达增加，导致DNA甲基化水平全面降低。而关于非跃变型果实成熟过程中DNA甲基化的动态变化以及生物学功能还不是很清楚。本文中，作者构建了未成熟和成熟草莓的单碱基高分辨率DNA甲基化图谱。试验结果显示在草莓过程成熟过程中，DNA甲基化水平降低。因此，成熟诱导的DNA低甲基化并不只是在跃变型果实中才有，非跃变型果实也是同样的情况。外施DNA甲基化抑制剂会引起过早的成熟表型，说明DNA低甲基化对于草莓的果实成熟是非常重要的。番茄和草莓果实成熟中DNA低甲基化潜在的分子机制是不同的。与番茄不同，在草莓成熟过程中DNA去甲基化酶的表达并没有上调。相反，草莓成熟过程中RdDM通路相关基因的表达下调。此外，成熟诱导的DNA低甲基化与siRNA水平降低有关，与RdDM活性降低一致。因此，作者推测RdDM的下调作用于草莓成熟过程中的DNA低甲基化。作者的研究为非跃变型果实成熟过程中DNA甲基化动态提供了新的视野，并且揭示了RdDM在调控植物重要发育过程发挥作用。

通讯：郎曌博  (http://www.psc.ac.cn/zjj.asp?id=84)

个人简介：2005-2009年，北京师范大学，生物学学士；2009-2010年，加利福利亚大学，植物遗传学硕士；2011-2014年，普渡大学，植物遗传学博士；2014-2016年，普渡大学，博士后。

研究方向：果实发育及表观遗传学。

doi: https://doi.org/10.1186/s13059-018-1587-x

Journal: Genome Biology

Published date: 04 December, 2018