ArticleBMC plant biology2014
Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice.
Article in BMC plant biology, 2014. 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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Who cites it
19 citing papers in PubMed, 34 citations in OpenAlex.
- The biogenesis, regulation and functions of transitive siRNA in plants.Acta biochimica et biophysica Sinica · 2024Review
- Gene Expression Analysis of Different Organs and Identification of AP2 Transcription Factors in Flax (Plants (Basel, Switzerland) · 2023Article
- Comprehensive Analysis of Differentially Expressed Genes and Epigenetic Modification-Related Expression Variation Induced by Saline Stress at Seedling Stage in Fiber and Oil Flax,Plants (Basel, Switzerland) · 2022Article
- Analysis of the RNA-Dependent RNA Polymerase 1 (RDR1) Gene Family in Melon.Plants (Basel, Switzerland) · 2022Article
- Alkaline Stress Induces Different Physiological, Hormonal and Gene Expression Responses in Diploid and Autotetraploid Rice.International journal of molecular sciences · 2022Article
- Absence of major epigenetic and transcriptomic changes accompanying an interspecific cross between peach and almond.Horticulture research · 2022Article
- Article
- Essential role of γ-clade RNA-dependent RNA polymerases in rice development and yield-related traits is linked to their atypical polymerase activities regulating specific genomic regions.The New phytologist · 2021Article
- RNA-dependent RNA polymerase 1 delays the accumulation of viroids in infected plants.Molecular plant pathology · 2021Article
- Role of non-coding RNAs in plant immunity.Plant communications · 2021Review
- Contribution of Small RNA Pathway to Interactions of Rice with Pathogens and Insect Pests.Rice (New York, N.Y.) · 2021Review
- Alterations of Rice (International journal of molecular sciences · 2020Article
- Dynamics of a geminivirus-encoded pre-coat protein and host RNA-dependent RNA polymerase 1 in regulating symptom recovery in tobacco.Journal of experimental botany · 2018Article
- Differential expression of cucumber RNA-dependent RNA polymerase 1 genes during antiviral defence and resistance.Molecular plant pathology · 2018Article
- A Signaling Cascade from miR444 to RDR1 in Rice Antiviral RNA Silencing Pathway.Plant physiology · 2016Article
- Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine.Scientific reports · 2016Article
- Roles and programming of Arabidopsis ARGONAUTE proteins during Turnip mosaic virus infection.PLoS pathogens · 2015Article
- Transcriptomic analysis of fruit stored under cold conditions using controlled atmosphere in Prunus persica cv. "Red Pearl".Frontiers in plant science · 2015Article
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Authors and funding
14 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEndogenous small (sm) RNAs (primarily si- and miRNAs) are important trans/cis-acting regulators involved in diverse cellular functions. In plants, the RNA-dependent RNA polymerases (RDRs) are essential for smRNA biogenesis. It has been established that RDR2 is involved in the 24 nt siRNA-dependent RNA-directed DNA methylation (RdDM) pathway. Recent studies have suggested that RDR1 is involved in a second RdDM pathway that relies mostly on 21 nt smRNAs and functions to silence a subset of genomic loci that are usually refractory to the normal RdDM pathway in Arabidopsis. Whether and to what extent the homologs of RDR1 may have similar functions in other plants remained unknown.
resultsWe characterized a loss-of-function mutant (Osrdr1) of the OsRDR1 gene in rice (Oryza sativa L.) derived from a retrotransposon Tos17 insertion. Microarray analysis identified 1,175 differentially expressed genes (5.2% of all expressed genes in the shoot-tip tissue of rice) between Osrdr1 and WT, of which 896 and 279 genes were up- and down-regulated, respectively, in Osrdr1. smRNA sequencing revealed regional alterations in smRNA clusters across the rice genome. Some of the regions with altered smRNA clusters were associated with changes in DNA methylation. In addition, altered expression of several miRNAs was detected in Osrdr1, and at least some of which were associated with altered expression of predicted miRNA target genes. Despite these changes, no phenotypic difference was identified in Osrdr1 relative to WT under normal condition; however, ephemeral phenotypic fluctuations occurred under some abiotic stress conditions.
conclusionsOur results showed that OsRDR1 plays a role in regulating a substantial number of endogenous genes with diverse functions in rice through smRNA-mediated pathways involving DNA methylation, and which participates in abiotic stress response.
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