热应激时 Sprague-Dawley 大鼠中长链非编码 RNA 的全基因组鉴定和功能预测。
Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress.
机构信息
Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, People's Republic of China.
Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
出版信息
BMC Genomics. 2021 Feb 17;22(1):122. doi: 10.1186/s12864-021-07421-8.
BACKGROUND
Heat stress (HS) is a major stress event in the life of an animal, with detrimental upshots in production and health. Long-non-coding RNAs (lncRNAs) play an important role in many biological processes by transcriptional regulation. However, no research has been reported on the characterization and functionality of lncRNAs in heat-stressed rats.
RESULTS
We studied expression levels of lncRNAs in rats during HS, using strand-specific RNA sequencing. Six rats, three in each of Control (22 ± 1 °C) and H120 (42 °C for 120 min) experimental groups, were used to screen for lncRNAs in their liver and adrenal glands. Totally, 4498 and 7627 putative lncRNAs were identified in liver and adrenal glands of the Control and H120 groups, respectively. The majority of lncRNAs were relatively shorter and contained fewer exons than protein-coding transcripts. In total, 482 (174 up-regulated and 308 down-regulated) and 271 (126 up-regulated and 145 down-regulated) differentially-expressed lncRNAs (DElncRNAs, P < 0.05) were identified in the liver and adrenal glands of the Control and H120 groups, respectively. Furthermore, 1274, 121, and 73 target differentially-expressed genes (DEGs) in the liver were predicted to interact with DElncRNAs based on trans-/cis- and sequence similarity regulatory modes. Functional annotation analyses indicated that these DEGs were mostly significantly enriched in insulin signalling, myeloid leukaemia, and glucagon signalling pathways. Similarly, 437, 73 and 41 target DEGs in the adrenal glands were mostly significantly enriched in the cell cycle (trans-prediction) and lysosome pathways (cis-prediction). The DElncRNAs interacting with DEGs that encode heat shock proteins (HSPs) may play an important role in HS response, which include Hsf4, Dnaja1, Dnajb4, Hsph1 and Hspb1 in the liver, and Dnajb13 and Hspb8 in the adrenal glands. The strand-specific RNA sequencing findings were also further verified through RT-qPCR.
CONCLUSIONS
This study is the first to provide a detailed characterization and functional analysis of expression levels of lncRNAs in liver and adrenal glands of heat-stressed rats, which provides basis for further studies on the biological functions of lncRNAs under heat stress in rats and other mammalian species.
背景
热应激（HS）是动物生命中的一个主要应激事件，对生产和健康产生不利影响。长链非编码 RNA（lncRNA）通过转录调控在许多生物学过程中发挥重要作用。然而，目前尚未有研究报道 lncRNA 在热应激大鼠中的特征和功能。
结果
我们使用链特异性 RNA 测序研究了 HS 期间大鼠肝脏和肾上腺中 lncRNA 的表达水平。使用 6 只大鼠，每组 3 只，分别在对照（22±1°C）和 H120（42°C 120 分钟）实验组中筛选。总共在对照组和 H120 组的肝脏和肾上腺中分别鉴定出 4498 和 7627 个潜在的 lncRNA。大多数 lncRNA 相对较短，所含外显子少于编码蛋白的转录本。总共在对照组和 H120 组的肝脏和肾上腺中分别鉴定出 482（174 个上调和 308 个下调）和 271（126 个上调和 145 个下调）个差异表达的 lncRNA（DElncRNA，P<0.05）。此外，基于顺式-反式和序列相似性调节模式，预测了 1274、121 和 73 个肝脏差异表达基因（DEG）的 1274、121 和 73 个靶标 DEG 与 DElncRNA 相互作用。功能注释分析表明，这些 DEG 主要显著富集于胰岛素信号、髓样白血病和胰高血糖素信号通路。同样，在肾上腺中，437、73 和 41 个靶标 DEG 主要显著富集于细胞周期（反式预测）和溶酶体途径（顺式预测）。与编码热休克蛋白（HSPs）的 DEG 相互作用的 DElncRNA 可能在 HS 反应中发挥重要作用，其中包括肝脏中的 Hsf4、Dnaja1、Dnajb4、Hsph1 和 Hspb1，以及肾上腺中的 Dnajb13 和 Hspb8。通过 RT-qPCR 进一步验证了链特异性 RNA 测序的结果。
结论
本研究首次提供了热应激大鼠肝脏和肾上腺中 lncRNA 表达水平的详细特征和功能分析，为进一步研究大鼠和其他哺乳动物热应激下 lncRNA 的生物学功能提供了基础。
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