title: Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.).
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: 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.
authors.forename: Yuanda
authors.initials: Y
authors.lastname: Lv
authors.affiliation: Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi, Mississippi State, USA.
authors.forename: Zhikai
authors.initials: Z
authors.lastname: Liang
authors.affiliation: Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
authors.forename: Min
authors.initials: M
authors.lastname: Ge
authors.affiliation: Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
authors.forename: Weicong
authors.initials: W
authors.lastname: Qi
authors.affiliation: Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
authors.forename: Tifu
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Lin
authors.affiliation: Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi, Mississippi State, USA. zp7@bch.msstate.edu.
authors.forename: Zhaohua
authors.initials: Z
authors.lastname: Peng
authors.affiliation: Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China. zhaohan@jaas.ac.cn.
authors.forename: Han
authors.initials: H
authors.lastname: Zhao
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D009584:Nitrogen / Q000378:metabolism*; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D062085:RNA, Long Noncoding / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D012270:Ribosomes / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D003313:Zea mays / Q000235:genetics / Q000254:growth & development*
chemical_list: D062085:RNA, Long Noncoding; D018749:RNA, Plant; D009584:Nitrogen
keywords: Coexpression network; Long noncoding RNA; Nitrogen response; RNA-Seq