Single-base methylome analysis reveals dynamic changes of genome-wide DNA methylation associated with rapid stem growth of woody bamboos
Single-base methylome analysis reveals dynamic changes of genome-wide DNA methylation associated with rapid stem growth of woody bamboos
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DOI：
10.1007/s00425-022-03962-8
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发表时间：
2022-08
期刊：
影响因子：
4.3
通讯作者：
Liang-Zhong Niu;Wei Xu;Peng‐Fei Ma;Zhen-Hua Guo;De‐Zhu Li
中科院分区：
文献类型：
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作者：
Liang-Zhong Niu;Wei Xu;Peng‐Fei Ma;Zhen-Hua Guo;De‐Zhu Li
主要结论：在新梢快速生长期（ST 2-ST 4），CG和CHG甲基化水平明显降低，可能是调控新梢快速生长过程中节间伸长的重要因素，而CHH甲基化水平与新梢发育时间或年龄密切相关。木质竹具有一个独特的特性，即在笋期，茎的快速生长是由节间伸长引起的。然而，DNA甲基化是否显著控制竹茎的快速生长仍不清楚。在这里，我们提出了全基因组DNA甲基化的古热带木本竹Bonia amplexicaulisat五个新定义的阶段，命名为ST 1-ST 5的芽生长。我们发现，CG和CHG甲基化水平在快速芽生长阶段（ST 2-ST 4）显着低于在孵化（ST 1）和平台期（ST 5）。甲基化水平的变化主要发生在基因的侧翼区和基因体区域，在ST 1和快速生长期（ST 2-ST 4）共鉴定出23647个差异甲基化区域（DMR）。结合转录组分析，我们发现DMR相关基因富集在生长素和茉莉酸（JA）信号转导等与植物生长密切相关的途径中。有趣的是，CHH甲基化不参与芽的快速生长，但通过在转座因子（TEs）区域逐渐积累与芽的发育时间密切相关。总的来说，我们的研究结果揭示了DNA甲基化在调控竹笋快速生长中的重要性，并表明DNA甲基化在木本竹中的作用与发育时间或年龄有关。
Main conclusionCG and CHG methylation levels in the rapid shoot growth stages (ST2–ST4) of woody bamboos were obviously decreased, which might regulate the internode elongation during rapid shoot growth, while CHH methylation was strongly associated with shoot developmental time or age.AbstractDNA methylation plays a critical role in the regulation of plant growth and development. Woody bamboos have a unique trait of rapid stem growth resulted from internode elongation at the shooting period. However, it is still unclear whether DNA methylation significantly controls the bamboo rapid stem growth. Here we present whole-genome DNA methylation profiles of the paleotropical woody bambooBonia amplexicaulisat five newly defined stages of shoot growth, named ST1–ST5. We found that CG and CHG methylation levels in the rapid shoot growth stages (ST2–ST4) were significantly lower than in the incubation (ST1) and plateau stages (ST5). The changes in methylation levels mainly occurred in flanking regions of genes and gene body regions, and 23647 differentially methylated regions (DMRs) were identified between ST1 and rapid shoot growth stages (ST2–ST4). Combined with transcriptome analysis, we found that DMR-related genes enriched in the auxin and jasmonic acid (JA) signal transduction, and other pathways closely related to plant growth. Intriguingly, CHH methylation was not involved in the rapid shoot growth, but strongly associated with shoot developmental time by gradually accumulating in transposable elements (TEs) regions. Overall, our results reveal the importance of DNA methylation in regulating the bamboo rapid shoot growth and suggest a role of DNA methylation associated with development time or age in woody bamboos.