Abiotic stress-induced DNA methylation in transposable elements and their transcripts reveals a multi-layered response in Moso bamboo

IF 6.2 1区农林科学 Q1 AGRICULTURAL ENGINEERING

Industrial Crops and Products Pub Date : 2024-02-07 DOI:10.1016/j.indcrop.2024.118108

Yiqian Ding , Long-Hai Zou , Muthusamy Ramakrishnan , Yujing Chen , Bailiang Zhu , Lu Yu , Mingbing Zhou

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引用次数: 0

Abstract

This study investigated the stress-induced epigenetic changes of transposable elements (TEs), TE-derived long non-coding RNAs (TE-lncRNAs), and TE-derived circular RNA (TE-circRNAs) in Moso bamboo seedlings exposed to various abiotic stresses. Long terminal repeat (LTR) retrotransposons and terminal inverted repeat (TIR) transposons exhibited higher levels of CG and CHG methylation within their bodies compared with their flanking regions. Ty1/copia and Ty3/gypsy retrotransposons exhibited similar methylation patterns in the LTR and coding regions. Conversely, MULE, hAT, and ENspm transposons displayed a trend of rising and then decreasing methylation patterns in the TIR regions. Stress-induced hypomethylation of coding regions enhanced the reactivation of TEs. Around 12.4% of lncRNAs and 11% of circRNAs were derived from TEs. TE-lncRNAs and TE-circRNAs were primarily derived from Ty1/copia and Ty3/gypsy superfamilies. No significant differences were observed in length distribution and expression patterns between TE-lincRNAs and non-TE-lincRNAs. In contrast, TE-circRNAs exhibited significantly higher expression levels compared with non-TE-circRNAs. TE-lncRNAs displayed stress-specific expression patterns, with tendencies for down-regulation under cold and salt stress and up-regulation under heat stress. TE-lncRNAs targeted various heat shock protein genes and heat stress transcription factor genes under heat stress condition. Gene network analysis revealed that Ph-TE-lncRNA3 and Ph-TE-circRNA3 play crucial roles in heat and UV stress response by regulating downstream genes. This study elucidates how TEs in Moso bamboo respond to stress and the role of TE-lncRNAs and TE-circRNAs in regulating stress tolerance.

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非生物胁迫诱导的转座元件 DNA 甲基化及其转录本揭示了毛竹的多层响应

本研究调查了暴露于各种非生物胁迫的毛竹幼苗中转座元件、转座元件衍生的长非编码RNA（TE-lncRNAs）和转座元件衍生的环状RNA（TE-circRNAs）的胁迫诱导表观遗传学变化。与侧翼区域相比，长末端重复（LTR）逆转录转座子和末端倒位重复（TIR）转座子在其体内表现出更高水平的CG和CHG甲基化。Ty1/copia 和 Ty3/gypsy 反转座子在 LTR 和编码区表现出相似的甲基化模式。相反，MULE、hAT 和 ENspm 转座子在 TIR 区域的甲基化模式呈现先上升后下降的趋势。应激诱导的编码区低甲基化增强了转座子的再激活。约有12.4%的lncRNA和11%的circRNA来源于TE。TE-lncRNA和TE-circRNA主要来自Ty1/copia和Ty3/gypsy超家族。TE-lincRNA与非TE-lincRNA在长度分布和表达模式上没有明显差异。相比之下，TE-circRNAs 的表达水平明显高于非 TE-circRNAs。TE-lncRNAs 的表达模式具有胁迫特异性，在冷胁迫和盐胁迫下呈下调趋势，而在热胁迫下呈上调趋势。在热胁迫条件下，TE-lncRNA以各种热休克蛋白基因和热胁迫转录因子基因为靶标。基因网络分析显示，Ph-TE-lncRNA3和Ph-TE-circRNA3通过调控下游基因在热胁迫和紫外胁迫响应中发挥关键作用。本研究阐明了毛竹中的TE如何应对胁迫，以及TE-lncRNA和TE-circRNA在调节胁迫耐受性中的作用。

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来源期刊

Industrial Crops and Products 农林科学-农业工程

CiteScore

9.50

自引率

8.50%

发文量

1518

审稿时长

43 days

期刊介绍： Industrial Crops and Products is an International Journal publishing academic and industrial research on industrial (defined as non-food/non-feed) crops and products. Papers concern both crop-oriented and bio-based materials from crops-oriented research, and should be of interest to an international audience, hypothesis driven, and where comparisons are made statistics performed.