Diversity and redundancy of the ripening regulatory networks revealed by the fruitENCODE and the new CRISPR/Cas9 CNR and NOR mutants
Diversity and redundancy of the ripening regulatory networks revealed by the fruitENCODE and the new CRISPR/Cas9 CNR and NOR mutants
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DOI：
10.1038/s41438-019-0122-x
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发表时间：
2019-02-11
影响因子：
8.7
通讯作者：
Qu, Guiqin
中科院分区：
文献类型：
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作者：
Gao, Ying;Zhu, Ning;Qu, Guiqin
番茄被认为是跃变型果实的遗传模型，其中三个主要参与者控制果实成熟过程：乙烯，成熟转录因子和DNA甲基化。fruitENCODE项目现在已经表明，在不同物种中有多种转录回路调节果实成熟，而H3 K27 me 3，而不是DNA甲基化，在限制这些成熟途径中发挥保守作用。此外，核心番茄成熟转录因子的功能现在受到质疑。我们采用CRISPR/Cas9基因组编辑来突变SBP-CNR和NAC-NOR转录因子，这两种转录因子都被认为是当前番茄成熟模型中的主调节因子。这些植物仅表现出延迟或部分非成熟表型，与原始突变体植物不同，原始突变体植物绝对不能成熟，这表明它们可能是功能获得型突变体。除了全基因组DNA甲基化增加外，原始突变体还在成熟基因位点如ACS 2、RIN和TDR 4中具有超H3 K27 me 3。很可能是多种遗传和表观遗传因素导致了它们强烈的非成熟表型。因此，我们建议该领域应该超越这些线性和二维模型，并接受这样一个事实，即重要的生物过程，如成熟，往往是由高度冗余的网络与输入来自多个层次。
Tomato is considered as the genetic model for climacteric fruits, in which three major players control the fruit ripening process: ethylene, ripening transcription factors, and DNA methylation. The fruitENCODE project has now shown that there are multiple transcriptional circuits regulating fruit ripening in different species, and H3K27me3, instead of DNA methylation, plays a conserved role in restricting these ripening pathways. In addition, the function of the core tomato ripening transcription factors is now being questioned. We have employed CRISPR/Cas9 genome editing to mutate the SBP-CNR and NAC-NOR transcription factors, both of which are considered as master regulators in the current tomato ripening model. These plants only displayed delayed or partial non-ripening phenotypes, distinct from the original mutant plants, which categorically failed to ripen, suggesting that they might be gain-of-function mutants. Besides increased DNA methylation genome-wide, the original mutants also have hyper-H3K27me3 in ripening gene loci such as ACS2, RIN, and TDR4. It is most likely that multiple genetic and epigenetic factors have contributed to their strong non-ripening phenotypes. Hence, we propose that the field should move beyond these linear and two dimensional models and embrace the fact that important biological processes such as ripening are often regulated by highly redundant network with inputs from multiple levels.