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

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

Author information

1
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.
2
School of Biological Sciences, the University of Hong Kong, Pokfulam Road, Hong Kong, China.
3
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.
4
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.

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

PMID:
27538394
PMCID:
PMC4991007
DOI:
10.1186/s12864-016-2929-2
[Indexed for MEDLINE]
Free PMC Article

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