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

BMC Genomics

Research Article

Zhikai Liang¹  Zhaohua Peng¹  Feng Lin²  Tifu Zhang²  Han Zhao²  Weicong Qi²  Min Ge²  Yuanda Lv³ 

[1] Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi, Mississippi State, USA;Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China;Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China;Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi, Mississippi State, USA;

关键词: RNA-Seq;    Long noncoding RNA;    Nitrogen response;    Coexpression network;   

DOI  :  10.1186/s12864-016-2650-1

 received in 2015-06-23, accepted in 2016-04-23,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundNitrogen (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.ResultsIn 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.ConclusionsWe 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.

【 授权许可】

CC BY   
© Lv et al. 2016