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Identification and characterization of long non-coding RNAs as competing endogenous RNAs in the cold stress response of Triticum aestivum.
Plant Biology ( IF 4.2 ) Pub Date : 2020-04-06 , DOI: 10.1111/plb.13119 Q Lu 1 , Q Xu 1 , F Guo 1 , Y Lv 1 , C Song 1 , M Feng 1 , J Yu 1 , D Zhang 1 , J Cang 1
中文翻译：
鉴定和鉴定长非编码RNAs在小麦的冷胁迫响应中是竞争性内源RNAs。
更新日期：2020-04-06
Plant Biology ( IF 4.2 ) Pub Date : 2020-04-06 , DOI: 10.1111/plb.13119 Q Lu 1 , Q Xu 1 , F Guo 1 , Y Lv 1 , C Song 1 , M Feng 1 , J Yu 1 , D Zhang 1 , J Cang 1
Affiliation
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- Long non‐coding RNAs (lncRNAs) play important roles in plant development and stress responses. MicroRNAs (miRNAs) are involved in transcriptional and post‐transcriptional gene regulation. It is not clear how lncRNA‐mediated plant responses to cold stress and how lncRNAs, miRNAs and target mRNAs cooperate subject to the competing endogenous RNA (ceRNA).
- We interpreted the function of lncRNAs in the winter wheat cultivar Dongnongdongmai 1 (Dn1). A total of 9970 putative lncRNAs were initially identified from three Dn1 lncRNA libraries (5 °C, −10 °C and −25 °C) using high‐throughput sequencing.
- Among the 14,626 genes detected via weighted gene co‐expression network analysis, 7435 lncRNAs were co‐expressed with 7191 mRNAs. We found six modules related to cold resistance in the lncRNA–mRNA weighted co‐expression network, and the functions of mRNAs were similar in each module. Antioxidant systems and hormones played important roles in low‐temperature responses. RNA sequencing analysis revealed that interactions between the 384 lncRNAs and 70 miRNAs were required for ceRNA activity. According to ceRNA activity, 225 lncRNAs, 60 miRNAs and 621 target mRNAs were involved in the regulatory networks of the cold stress response. Notably, a conserved region was found in the complementary regions of lncRNAs and miR164/408 but had reverse expression trends in the ceRNA network.
- Our results reveal possible roles of lncRNAs–mRNAs in the regulatory networks associated with tolerance to low temperature and provide useful information for more strategic use of genomic resources in wheat breeding.
中文翻译：
鉴定和鉴定长非编码RNAs在小麦的冷胁迫响应中是竞争性内源RNAs。
- 较长的非编码RNA（lncRNA）在植物发育和胁迫响应中发挥重要作用。MicroRNA（miRNA）参与转录和转录后基因调控。尚不清楚lncRNA介导的植物对冷胁迫的反应以及lncRNA，miRNA和靶标mRNA如何在竞争性内源RNA（ceRNA）的作用下协同作用。
- 我们解释了lncRNAs在冬小麦品种Dongnongdongmai 1（Dn1）中的功能。最初使用高通量测序从三个Dn1 lncRNA文库（5°C，-10°C和-25°C）中鉴定出总共9970个lncRNA。
- 通过加权基因共表达网络分析检测到的14,626个基因中，有7435个lncRNA与7191个mRNA共表达。我们在lncRNA-mRNA加权共表达网络中发现了六个与抗寒性相关的模块，每个模块中的mRNA功能相似。抗氧化剂系统和激素在低温反应中起重要作用。RNA测序分析表明384个lncRNA和70个miRNA之间的相互作用是ceRNA活性所必需的。根据ceRNA的活性，冷应激反应的调控网络涉及225个lncRNA，60个miRNA和621个靶mRNA。值得注意的是，在lncRNA和miR164 / 408的互补区域中发现了保守区域，但是在ceRNA网络中具有反向表达趋势。
- 我们的结果揭示了lncRNAs–mRNAs在与耐低温性相关的调控网络中的可能作用，并为小麦育种中基因组资源的更战略性利用提供了有用的信息。
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