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.

番茄被认为是更年期水果的遗传模型，其中三个主要因素控制着水果的成熟过程：乙烯，成熟的转录因子和DNA甲基化。fruitENCODE项目现已显示，在不同物种中存在多个调控果实成熟的转录回路，并且H3K27me3（而不是DNA甲基化）在限制这些成熟途径中起着保守的作用。另外，目前正在质疑核心番茄成熟转录因子的功能。我们已经使用CRISPR / Cas9基因组编辑来突变SBP - CNR和NAC - NOR转录因子，在当前的番茄成熟模型中，这两个因子均被视为主要调控因子。这些植物仅表现出延迟的或部分的非成熟表型，与原始突变体植物不同，后者完全无法成熟，表明它们可能是功能获得的突变体。除了在全基因组范围内增加DNA甲基化作用外，原始突变体还在ACS2，RIN和TDR4等成熟基因位点中具有hyper-H3K27me3。多种遗传和表观遗传因素最有可能促成了其强大的非成熟表型。因此，我们建议该领域应超越这些线性和二维模型，并接受这样一个事实，即重要的生物学过程（例如成熟）通常由高度冗余的网络进行调节，并具有来自多个级别的输入。