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Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.)

文献类型： 外文期刊

作者： Lv, Yuanda 1 ; Liang, Zhikai 2 ; Ge, Min 1 ; Qi, Weicong 1 ; Zhang, Tifu 1 ; Lin, Feng 1 ; Peng, Zhaohua 2 ; Zhao, Han 1 ;

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

2.Mississippi State Univ, Dept Biochem & Mol Biol, Mississippi State, MS 39762 USA

关键词： RNA-Seq;Long noncoding RNA;Nitrogen response;Coexpression 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： 2016 年 17 卷

页码：

收录情况： SCI

摘要： Background: Nitrogen (N) is an essential and often limiting nutrient to plant growth and development. Previous studies have shown that the mRNA expressions of numerous genes are regulated by nitrogen supplies; however, little is known about the expressed non-coding elements, for example long non-coding RNAs (lncRNAs) that control the response of maize (Zea mays L.) to nitrogen. LncRNAs are a class of non-coding RNAs larger than 200 bp, which have emerged as key regulators in gene expression. Results: In this study, we surveyed the intergenic/intronic lncRNAs in maize B73 leaves at the V7 stage under conditions of N-deficiency and N-sufficiency using ribosomal RNA depletion and ultra-deep total RNA sequencing approaches. By integration with mRNA expression profiles and physiological evaluations, 7245 lncRNAs and 637 nitrogen-responsive lncRNAs were identified that exhibited unique expression patterns. Co-expression network analysis showed that the nitrogen-responsive lncRNAs were enriched mainly in one of the three co-expressed modules. The genes in the enriched module are mainly involved in NADH dehydrogenase activity, oxidative phosphorylation and the nitrogen compounds metabolic process. Conclusions: We identified a large number of lncRNAs in maize and illustrated their potential regulatory roles in response to N stress. The results lay the foundation for further in-depth understanding of the molecular mechanisms of lncRNAs' role in response to nitrogen stresses.

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