Global increase in DNA methylation during orange fruit development and ripening

First author: Huan Huang; Affiliations: Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (中科院上海植物逆境生物学研究中心): Shanghai China

Corresponding author: Zhaobo Lang

DNA methylation is an important epigenetic mark involved in many biological processes. The genome of the climacteric tomato fruit undergoes a global loss of DNA methylation due to active DNA demethylation during the ripening process. It is unclear whether the ripening of other fruits is also associated with global DNA demethylation. We characterized the single-base resolution DNA methylomes of sweet orange fruits. Compared with immature orange fruits, ripe orange fruits gained DNA methylation at over 30,000 genomic regions and lost DNA methylation at about 1,000 genomic regions, suggesting a global increase in DNA methylation during orange fruit ripening. This increase in DNA methylation was correlated with decreased expression of DNA demethylase genes. The application of a DNA methylation inhibitor interfered with ripening, indicating that the DNA hypermethylation is critical for the proper ripening of orange fruits. We found that ripening-associated DNA hypermethylation was associated with the repression of several hundred genes, such as photosynthesis genes, and with the activation of hundreds of genes, including genes involved in abscisic acid responses. Our results suggest important roles of DNA methylation in orange fruit ripening.

DNA甲基化是参与许多重要生物学进程的表观标记。在跃变型番茄果实成熟过程中，由于DNA去甲基化酶的活跃，导致了全基因组范围上的DNA甲基化丢失。但其它水果的成熟过程中是否存在DNA去甲基化还不清楚。本文研究了甜橙单碱基分辨率的DNA甲基化组。与未成熟的甜橙相比，成熟的甜橙在超过30000个基因组区域存在DNA甲基化，而仅在1000个基因组区域DNA甲基化丢失，说明在甜橙果实成熟过程中DNA甲基化增加。甜橙成熟过程中DNA甲基化的增加与DNA去甲基化酶编码基因的下调相关。外施DNA甲基化抑制剂能够干扰甜橙的成熟过程，说明DNA超甲基化对于甜橙果实的成熟非常重要。作者发现成熟相关的DNA超甲基化与数百个基因的抑制相关，比如说某些光合基因，另外还与其它数百个基因的激活相关，包括参与脱落酸响应的相关基因。本文的研究结果揭示了DNA甲基化在甜橙果实成熟过程中发挥重要作用。

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/10.1073/pnas.1815441116

Journal: PNAS

Published date: January 11, 2019