| 從DNA甲基化看草莓與番茄的不同 | Genome Biology |
論文標題：Downregulation of RdDM during strawberry fruit ripening
期刊：Genome Biology
作者：Jingfei Cheng†, Qingfeng Niu†, Bo Zhang, Kunsong Chen, Ruihua Yang, Jian-Kang Zhu, Yijing Zhang and Zhaobo Lang
發表時間：2018/12/04
數字識別碼：10.1186/s13059-018-1587-x
原文連結：https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1587-x?utm_source=other&utm_medium=other&utm_content=null&utm_campaign=BSCN_2_DD_GenBio_Article_Scinet
微信連結：https://mp.weixin.qq.com/s/HSU3cmye01hUGCS52OXhbQ
中科院上海植物逆境中心郎曌博研究組在最近的一項研究中，通過整合分析不同成熟時期草莓的全基因組DNA甲基化圖譜、小RNA及轉錄組數據，揭示了DNA甲基化在草莓果實成熟過程中的調控作用。該研究發表在Genome Biology上。
DNA甲基化是真核生物中非常保守的表觀遺傳修飾，它參與調控基因表達、病原菌免疫、基因印記等多種生物學過程。最近研究表明, DNA甲基化參與調控肉質果實（Fleshy fruit）的成熟。肉質果實按照其成熟過程是否發生呼吸躍變分為呼吸躍變型果實（如番茄）和非呼吸躍變型果實（如草莓）。之前的研究表明，番茄果實在成熟的過程中，由於DNA去甲基化酶SlDML2的表達上調，引起了全基因組範圍內的DNA去甲基化變化，並且該變化對於果實正常成熟至關重要。但是在其他果實中，DNA甲基化是否參與調控果實成熟及其調控機制還不清楚。
圖片來自論文
中科院上海植物逆境中心郎曌博研究組此次發現，與番茄相似，草莓在成熟過程中發生基因組DNA甲基化降低現象；但同時他們的研究發現，草莓中DNA甲基化降低的分子機制與番茄中不同：番茄成熟過程中甲基化下調是由於去甲基化酶表達上調導致，而草莓中小RNA介導的DNA甲基化通路減弱則是甲基化下調的主要原因，並且成熟過程中小RNA表達下調也證實了RdDM活性的降低。該研究為定點修飾甲基化調控基因表達進而改良草莓性狀提供了潛在靶點。
郎曌博：
中科院上海植物逆境生物學中心研究員／博士生導師。先後於北京師範大學和美國普渡大學獲得生物學學士和植物遺傳學博士學位。主要研究方向為植物中的DNA甲基化調控機制以及生物學功能。具體研究內容包括果實成熟過程中的DNA甲基化調控機制，以及與植物激素轉錄因子的相互作用機理。
摘要：
Background
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.
Results
Here, we generate single-base resolution maps of the DNA methylome in immature 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.
Conclusions
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.
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https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1587-x?utm_source=other&utm_medium=other&utm_content=null&utm_campaign=BSCN_2_DD_GenBio_Article_Scinet
期刊介紹:
Genome Biology (https://genomebiology.biomedcentral.com/,13.2 - 2-year Impact Factor, 16.5 - 5-year Impact Factor) publishes outstanding research in all areas of biology and biomedicine studied from a genomic and post-genomic perspective.
The current impact factor is 13.214* and the journal is ranked 4th among research journals in the Genetics and Heredity category by Thomson Reuters. Genome Biology is the highest ranked open access journal in the category.
（來源：科學網）
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