Biochemistry, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Staudtstraße 5, 91058, Erlangen, Germany.
KWS SAAT SE & Co. KGaA, Grimsehlstraße 31, 37574, Einbeck, Germany.
BMC Genomics. 2022 Feb 17;23(1):144. doi: 10.1186/s12864-022-08312-2.
DNA methylation is thought to influence the expression of genes, especially in response to changing environmental conditions and developmental changes. Sugar beet (Beta vulgaris ssp. vulgaris), and other biennial or perennial plants are inevitably exposed to fluctuating temperatures throughout their lifecycle and might even require such stimulus to acquire floral competence. Therefore, plants such as beets, need to fine-tune their epigenetic makeup to ensure phenotypic plasticity towards changing environmental conditions while at the same time steering essential developmental processes. Different crop species may show opposing reactions towards the same abiotic stress, or, vice versa, identical species may respond differently depending on the specific kind of stress.
In this study, we investigated common effects of cold treatment on genome-wide DNA methylation and gene expression of two Beta vulgaris accessions via multi-omics data analysis. Cold exposure resulted in a pronounced reduction of DNA methylation levels, which particularly affected methylation in CHH context (and to a lesser extent CHG) and was accompanied by transcriptional downregulation of the chromomethyltransferase CMT2 and strong upregulation of several genes mediating active DNA demethylation.
Integration of methylomic and transcriptomic data revealed that, rather than methylation having directly influenced expression, epigenetic modifications correlated with changes in expression of known players involved in DNA (de)methylation. In particular, cold triggered upregulation of genes putatively contributing to DNA demethylation via the ROS1 pathway. Our observations suggest that these transcriptional responses precede the cold-induced global DNA-hypomethylation in non-CpG, preparing beets for additional transcriptional alterations necessary for adapting to upcoming environmental changes.
DNA 甲基化被认为会影响基因的表达，尤其是在应对环境变化和发育变化时。糖甜菜（Beta vulgaris ssp. vulgaris）和其他二年生或多年生植物在其生命周期中不可避免地会受到温度波动的影响，甚至可能需要这种刺激来获得花的能力。因此，像甜菜这样的植物需要精细地调整其表观遗传组成，以确保对环境变化的表型可塑性，同时引导必要的发育过程。不同的作物物种可能对同一非生物胁迫表现出相反的反应，或者相反，相同的物种可能因特定的胁迫而表现出不同的反应。
在这项研究中，我们通过多组学数据分析研究了冷处理对两个甜菜品种全基因组 DNA 甲基化和基因表达的共同影响。冷暴露导致 DNA 甲基化水平显著降低，这尤其影响了 CHH 环境（以及在较小程度上影响 CHG）的甲基化，同时伴随着染色质甲基转移酶 CMT2 的转录下调和几个介导主动 DNA 去甲基化的基因的强烈上调。
甲基组学和转录组学数据的整合表明，DNA 甲基化并非直接影响基因表达，而是与已知参与 DNA（去）甲基化的表观遗传修饰相关。特别是，冷胁迫触发了通过 ROS1 途径可能有助于 DNA 去甲基化的基因的上调。我们的观察表明，这些转录反应先于冷诱导的非 CpG 区的全基因组 DNA 低甲基化，使甜菜为适应即将到来的环境变化而进行额外的转录改变做好准备。
