title: Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors: Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang, 25354, Korea.
authors: Pil Joong
authors: PJ
authors: Chung
authors: Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang, 25354, Korea.
authors: Harin
authors: H
authors: Jung
authors: Department of Life Science, Hallym University, Chuncheon, 24252, Korea.
authors: Dong-Hoon
authors: DH
authors: Jeong
authors: Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, Korea.
authors: Sun-Hwa
authors: SH
authors: Ha
authors: Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang, 25354, Korea.|Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea.
authors: Yang Do
authors: YD
authors: Choi
authors: Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang, 25354, Korea. jukon@snu.ac.kr.
authors: Ju-Kon
authors: JK
authors: Kim
mesh_terms: D000220:Adaptation, Biological; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D035683:MicroRNAs / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D034622:RNA Interference; D016372:RNA, Antisense / Q000235:genetics; D022661:RNA, Untranslated; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D016372:RNA, Antisense; D022661:RNA, Untranslated
keywords: Drought stress; Non-coding RNA; Oryza sativa; Putative target genes; RNA-seq; lncRNAs; miRNA