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Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

Cited 44 time in Web of Science Cited 41 time in Scopus
Authors
Chung, Pil Joong; Jung, Harin; Jeong, Dong-Hoon; Ha, Sun-Hwa; Choi, Yang Do; Kim, Ju-Kon
Issue Date
2016-08-08
Publisher
BioMed Central
Citation
BMC Genomics, 17(1):563
Keywords
Oryza sativaDrought stresslncRNAsmiRNANon-coding RNAPutative target genesRNA-seq
Description
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Abstract
Background
Plant transcriptome profiling has provided a tool for understanding the mechanisms by which plants respond to stress conditions. Analysis of genome-wide transcriptome will provides a useful dataset of drought responsive noncoding RNAs and their candidate target genes that may be involved in drought stress responses.

Results
Here RNA-seq analyses of leaves from drought stressed rice plants was performed, producing differential expression profiles of noncoding RNAs. We found that the transcript levels of 66 miRNAs changed significantly in response to drought conditions and that they were negatively correlated with putative target genes during the treatments. The negative correlations were further validated by qRT-PCR using total RNAs from both drought-treated leaves and various tissues at different developmental stages. The drought responsive miRNA/target pairs were confirmed by the presence of decay intermediates generated by miRNA-guided cleavages in Parallel Analysis of RNA Ends (PARE) libraries. We observed that the precursor miR171f produced two different mature miRNAs, miR171f-5p and miR171f-3p with 4 candidate target genes, the former of which was responsive to drought conditions. We found that the expression levels of the miR171f precursor negatively correlated with those of one candidate target gene, but not with the others, suggesting that miR171f-5p was drought-responsive, with Os03g0828701-00 being a likely target. Pre-miRNA expression profiling indicated that miR171f is involved in the progression of rice root development and growth, as well as the response to drought stress. Ninety-eight lncRNAs were also identified, together with their corresponding antisense transcripts, some of which were responsive to drought conditions.

Conclusions
We identified rice noncoding RNAs (66 miRNAs and 98 lncRNAs), whose expression was highly regulated by drought stress conditions, and whose transcript levels negatively correlated with putative target genes.
Language
English
URI
https://hdl.handle.net/10371/100484
DOI
https://doi.org/10.1186/s12864-016-2997-3
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College of Agriculture and Life Sciences (농업생명과학대학)Program in Agricultural Biotechnology (협동과정-농업생물공학전공)Journal Papers (저널논문_협동과정-농업생물공학전공)
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