ArticlePloS one2015
Genome-Wide Dissection of the MicroRNA Expression Profile in Rice Embryo during Early Stages of Seed Germination.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed, 32 citations in OpenAlex.
- Improved Degradome Sequencing Protocol via Reagent Recycling from sRNAseq Library Preparations.International journal of molecular sciences · 2025Article
- Genome-Wide Association-Based Identification of Alleles, Genes and Haplotypes Influencing Yield in Rice (International journal of molecular sciences · 2024Article
- The involvement and therapeutic potential of lncRNA Kcnq1ot1/miR-34a-5p/Sirt1 pathway in arsenic trioxide-induced cardiotoxicity.Journal of translational medicine · 2023Article
- StandardizedFrontiers in pharmacology · 2023Article
- Analysis of gene expression in early seed germination of rice: landscape and genetic regulation.BMC plant biology · 2022Article
- Review
- Metabolic Changes in Seed Embryos of Hypoxia-Tolerant Rice and Hypoxia-Sensitive Barley at the Onset of Germination.Plants (Basel, Switzerland) · 2021Article
- Reproductive phasiRNA loci and DICER-LIKE5, but not microRNA loci, diversified in monocotyledonous plants.Plant physiology · 2021Article
- The role of RNA-binding protein, microRNA and alternative splicing in seed germination: a field need to be discovered.BMC plant biology · 2021Review
- Barley Seeds miRNome Stability during Long-Term Storage and Aging.International journal of molecular sciences · 2021Article
- Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.).BMC genomics · 2019Article
- Verification of miRNAs in ginseng decoction by high-throughput sequencing and quantitative real-time PCR.Heliyon · 2019Article
- RicetissueTFDB: A Genome-Wide Identification of Tissue-Specific Transcription Factors in Rice.The plant genome · 2019Article
- Transcriptional networks orchestrating programmed cell death during plant development.Current topics in developmental biology · 2019Review
- Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination.Scientific reports · 2018Article
- Identification of exosome-like nanoparticle-derived microRNAs from 11 edible fruits and vegetables.PeerJ · 2018Article
- Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species.BMC genomics · 2017Article
- Systems biology and genome-wide approaches to unveil the molecular players involved in the pre-germinative metabolism: implications on seed technology traits.Plant cell reports · 2017Review
- Small RNA and degradome profiling reveals miRNA regulation in the seed germination of ancient eudicot Nelumbo nucifera.BMC genomics · 2016Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The first 24 hours after imbibition (HAI) is pivotal for rice seed germination, during which embryo cells switch from a quiescent state to a metabolically active state rapidly. MicroRNAs (miRNAs) have increasingly been shown to play important roles in rice development. Nevertheless, limited knowledge about miRNA regulation has been obtained in the early stages of rice seed germination. In this study, the small RNAs (sRNAs) from embryos of 0, 12, and 24 HAI rice seeds were sequenced to investigate the composition and expression patterns of miRNAs. The bioinformatics analysis identified 289 miRNA loci, including 59 known and 230 novel miRNAs, and 35 selected miRNAs were confirmed by stem-loop real-time RT-PCR. Expression analysis revealed that the dry and imbibed seeds have unique miRNA expression patterns compared with other tissues, particularly for the dry seeds. Using three methods, Mireap, psRNATarget and degradome analyses, 1197 potential target genes of identified miRNAs involved in various molecular functions were predicted. Among these target genes, 39 had significantly negative correlations with their corresponding miRNAs as inferred from published transcriptome data, and 6 inversely expressed miRNA-target pairs were confirmed by 5'-RACE assay. Our work provides an inventory of miRNA expression profiles and miRNA-target interactions in rice embryos, and lays a foundation for further studies of miRNA-mediated regulation in initial seed germination.
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