ArticleBMC genomics2018
Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Strigolactone, reactive oxygen species, abscisic acid, and miR399 pathway in tobacco host plant regulate growth of parasitizing broomrape Phelipanche aegyptiaca during nitrogen or phosphorous stress.BMC plant biology · 2026Article
- MicroRNA and target gene dynamics in potato under nitrogen deficiency.Scientific reports · 2025Article
- LncRNA-mediated early regulatory networks in sugar beet (Beta vulgaris L.) response to low nitrogen.BMC genomics · 2025Article
- MicroRNA gatekeepers: Orchestrating rhizospheric dynamics.Journal of integrative plant biology · 2025Review
- Ammonium Transporter 1 (Current issues in molecular biology · 2025Article
- Silencing of miR169a improves drought stress by enhancing vascular architecture, ROS scavenging, and photosynthesis ofFrontiers in plant science · 2025Article
- Biological Insights and Recent Advances in Plant Long Non-Coding RNA.International journal of molecular sciences · 2024Review
- MicroRNAs as potent regulators in nitrogen and phosphorus signaling transduction and their applications.Stress biology · 2024Review
- MicroRNAs Participate in Morphological Acclimation of Sugar Beet Roots to Nitrogen Deficiency.International journal of molecular sciences · 2024Article
- Underground communication: Long non-coding RNA signaling in the plant rhizosphere.Plant communications · 2024Review
- Switching action modes of miR408-5p mediates auxin signaling in rice.Nature communications · 2024Article
- CcNFYB3-CcMATE35 and LncRNA CcLTCS-CcCS modules jointly regulate the efflux and synthesis of citrate to enhance aluminium tolerance in pigeon pea.Plant biotechnology journal · 2024Article
- Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Roots of Rice Seedlings under Nitrogen Deficiency.Plants (Basel, Switzerland) · 2023Article
- Transcriptome analysis reveals a lncRNA-miRNA-mRNA regulatory network in OsRpp30-mediated disease resistance in rice.BMC genomics · 2023Article
- Non-Targeted Metabolomic Analysis ofMetabolites · 2023Article
- Pokkali: A Naturally Evolved Salt-Tolerant Rice Shows a Distinguished Set of lncRNAs Possibly Contributing to the Tolerant Phenotype.International journal of molecular sciences · 2023Article
- Transcriptomic and Physiological Analyses of Two Rice Restorer Lines under Different Nitrogen Supplies Provide Novel Insights into Hybrid Rice Breeding.Plants (Basel, Switzerland) · 2023Article
- Long term nitrogen deficiency alters expression of miRNAs and alters nitrogen metabolism and root architecture in Indian dwarf wheat (Triticum sphaerococcum Perc.) genotypes.Scientific reports · 2023Article
- Transcriptome Profiling and Chlorophyll Metabolic Pathway Analysis Reveal the Response ofPlants (Basel, Switzerland) · 2023Article
- Contribution of RdDM to the ecotype-specific differential methylation on conserved as well as highly variable regions between Arabidopsis ecotypes.BMC genomics · 2023Article
8 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
backgroundNitrogen (N) is a key macronutrient essential for plant growth, and its availability has a strong influence on crop development. The application of synthetic N fertilizers on crops has increased substantially in recent decades; however, the applied N is not fully utilized due to the low N use efficiency of crops. To overcome this limitation, it is important to understand the genome-wide responses and functions of key genes and potential regulatory factors in N metabolism.
resultsHere, we characterized changes in the rice (Oryza sativa) transcriptome, including genes, newly identified putative long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) and their target mRNAs in response to N starvation using four different transcriptome approaches. Analysis of rice genes involved in N metabolism and/or transport using strand-specific RNA-Seq identified 2588 novel putative lncRNA encoding loci. Analysis of previously published RNA-Seq datasets revealed a group of N starvation-responsive lncRNAs showing differential expression under other abiotic stress conditions. Poly A-primed sequencing (2P-Seq) revealed alternatively polyadenylated isoforms of N starvation-responsive lncRNAs and provided precise 3' end information on the transcript models of these lncRNAs. Analysis of small RNA-Seq data identified N starvation-responsive miRNAs and down-regulation of miR169 family members, causing de-repression of NF-YA, as confirmed by strand-specific RNA-Seq and qRT-PCR. Moreover, we profiled the N starvation-responsive down-regulation of root-specific miRNA, osa-miR444a.4-3p, and Degradome sequencing confirmed MADS25 as a novel target gene.
conclusionsIn this study, we used a combination of multiple RNA-Seq analyses to extensively profile the expression of genes, newly identified lncRNAs, and microRNAs in N-starved rice roots and shoots. Data generated in this study provide an in-depth understanding of the regulatory pathways modulated by N starvation-responsive miRNAs. The results of comprehensive, large-scale data analysis provide valuable information on multiple aspects of the rice transcriptome, which may be useful in understanding the responses of rice plants to changes in the N supply status of soil.
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