Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana

BMC Genomics. 2016 Aug 18;17:655. doi: 10.1186/s12864-016-2929-2.

Abstract

Background: 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.

Results: 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.

Conclusions: Altogether, our data provide a rich resource of candidate lncRNAs involved in the Pi starvation regulatory network.

Keywords: Arabidopsis thaliana; Long ncRNAs; Phosphate starvation; Poly(A)+; Poly(A)–; RNA-Seq.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis / growth & development*
  • Arabidopsis Proteins / genetics
  • Computational Biology / methods
  • Gene Expression Regulation, Plant
  • Gene Regulatory Networks
  • Phosphates / metabolism*
  • Plant Roots / genetics
  • RNA, Long Noncoding / genetics*
  • Seedlings / genetics
  • Sequence Analysis, RNA / methods*

Substances

  • Arabidopsis Proteins
  • Phosphates
  • RNA, Long Noncoding