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Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response

文献类型： 外文期刊

作者： Lv, Yuanda 1 ; Hu, Fengqin 3 ; Zhou, Yongfeng 2 ; Wu, Feilong 4 ; Gaut, Brandon S. 2 ;

作者机构： 1.Jiangsu Acad Agr Sci, Inst Crop Germplasm & Biotechnol, Prov Key Lab Agrobiol, Nanjing, Jiangsu, Peoples R China

2.UC Irvine, Dept Ecol & Evolutionary, Biol, Irvine, CA 92697 USA

3.Chinese Acad Sci, Inst Soil Sci, Nanjing, Jiangsu, Peoples R China

4.UC Irvine, Dept Civil & Environm, Engn, Irvine, CA USA

关键词： Long non-coding RNA; Transposable elements; Abiotic stress; Co-expression network

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2019 年 20 卷 1 期

页码：

收录情况： SCI

摘要： Background Several studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic stress response. However, our understanding of the complement, function and origin of lncRNAs - and especially transposon derived lncRNAs (TE-lncRNAs) - in response to abiotic stress is still in its infancy. Results We utilized a dataset of 127 RNA sequencing samples that included total RNA datasets and PacBio fl-cDNA data to discover lncRNAs in maize. Overall, we identified 23,309 candidate lncRNAs from polyA+ and total RNA samples, with a strong discovery bias within total RNA. The majority (65%) of the 23,309 lncRNAs had sequence similarity to transposable elements (TEs). Most had similarity to long-terminal-repeat retrotransposons from the Copia and Gypsy superfamilies, reflecting a high proportion of these elements in the genome. However, DNA transposons were enriched for lncRNAs relative to their genomic representation by 2-fold. By assessing the fraction of lncRNAs that respond to abiotic stresses like heat, cold, salt and drought, we identified 1077 differentially expressed lncRNA transcripts, including 509 TE-lncRNAs. In general, the expression of these lncRNAs was significantly correlated with their nearest gene. By inferring co-expression networks across our large dataset, we found that 39 lncRNAs are as major hubs in co-expression networks that respond to abiotic stress, and 18 appear to be derived from TEs. Conclusions Our results show that lncRNAs are enriched in total RNA samples, that most (65%) are derived from TEs, that at least 1077 are differentially expressed during abiotic stress, and that 39 are hubs in co-expression networks, including a small number that are evolutionary conserved. These results suggest that lncRNAs, including TE-lncRNAs, may play key regulatory roles in moderating abiotic responses.

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