title: Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana.
abstract: Previously, several long non-coding RNAs (lncRNAs) were characterized as regulators in phosphate (Pi) starvation responses. However, systematic studies of novel lncRNAs involved in the Pi starvation signaling pathways have not been reported.
  
  
  
  Here, we used a genome-wide sequencing and bioinformatics approach to identify both poly(A) + and poly(A)- lncRNAs that responded to Pi starvation in Arabidopsis thaliana. We sequenced shoot and root transcriptomes of the Arabidopsis seedlings grown under Pi-sufficient and Pi-deficient conditions, and predicted 1212 novel lncRNAs, of which 78 were poly(A)- lncRNAs. By employing strand-specific RNA libraries, we discovered many novel antisense lncRNAs for the first time. We further defined 309 lncRNAs that were differentially expressed between P+ and P- conditions in either shoots or roots. Through Gene Ontology enrichment of the associated protein-coding genes (co-expressed or close on the genome), we found that many lncRNAs were adjacent or co-expressed with the genes involved in several Pi starvation related processes, including cell wall organization and photosynthesis. In total, we identified 104 potential lncRNA targets of PHR1, a key regulator for transcriptional response to Pi starvation. Moreover, we identified 16 candidate lncRNAs as potential targets of miR399, another key regulator of plant Pi homeostasis.
  
  
  
  Altogether, our data provide a rich resource of candidate lncRNAs involved in the Pi starvation regulatory network.
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Center for Synthetic and Systems Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
authors.forename: Jiapei
authors.initials: J
authors.lastname: Yuan
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Center for Synthetic and Systems Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Center for Synthetic and Systems Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
authors.forename: Jinsong
authors.initials: J
authors.lastname: Dong
authors.affiliation: School of Biological Sciences, the University of Hong Kong, Pokfulam Road, Hong Kong, China.
authors.forename: Yuzhe
authors.initials: Y
authors.lastname: Sun
authors.affiliation: School of Biological Sciences, the University of Hong Kong, Pokfulam Road, Hong Kong, China.
authors.forename: Boon L
authors.initials: BL
authors.lastname: Lim
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Center for Synthetic and Systems Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. liu-d@tsinghua.edu.cn.
authors.forename: Dong
authors.initials: D
authors.lastname: Liu
authors.affiliation: MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Center for Synthetic and Systems Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. zhilu@tsinghua.edu.cn.
authors.forename: Zhi John
authors.identifier: 0000-0003-4751-9400
authors.initials: ZJ
authors.lastname: Lu
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development*; D029681:Arabidopsis Proteins / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D010710:Phosphates / Q000378:metabolism*; D018517:Plant Roots / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D036226:Seedlings / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D029681:Arabidopsis Proteins; D010710:Phosphates; D062085:RNA, Long Noncoding
keywords: Arabidopsis thaliana; Long ncRNAs; Phosphate starvation; Poly(A)+; Poly(A)–; RNA-Seq