ArticleGenomics, proteomics & bioinformatics2013
Comparative analysis of microRNA promoters in Arabidopsis and rice.
Article in Genomics, proteomics & bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 26 citations in OpenAlex.
- Integration of phytohormones, miRNAs and transcriptome sequencing in cucumber fruit development under high-temperature stress.Food chemistry. Molecular sciences · 2026Article
- miR828 positively regulates proanthocyanidin accumulation in sainfoin (Onobrychis viciifolia).BMC plant biology · 2026Article
- Functional Characterization of a Root-Preferential and Stress-Inducible Promoter of Eca-miR482f inPlants (Basel, Switzerland) · 2025Article
- Transcriptional Regulation of zma-International journal of molecular sciences · 2022Article
- Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis.Genomics, proteomics & bioinformatics · 2022Article
- MicroRNAs Are Involved in Regulating Plant Development and Stress Response through Fine-Tuning of TIR1/AFB-Dependent Auxin Signaling.International journal of molecular sciences · 2022Review
- Small Non-Coding RNAs at the Crossroads of Regulatory Pathways Controlling Somatic Embryogenesis in Seed Plants.Plants (Basel, Switzerland) · 2021Review
- The Critical Role of Small RNAs in Regulating Plant Innate Immunity.Biomolecules · 2021Review
- Molecular characterization of miRNA genes and their expression in Dimocarpus longan Lour.Planta · 2021Article
- Profiling the Abiotic Stress Responsive microRNA Landscape ofPlants (Basel, Switzerland) · 2019Article
- Conservation and diversification of the miR166 family in soybean and potential roles of newly identified miR166s.BMC plant biology · 2017Article
- MicroRNAs Are Intensively Regulated during Induction of Somatic Embryogenesis in Arabidopsis.Frontiers in plant science · 2017Article
- Promoter methylation regulates the abundance of osa-miR393a in contrasting rice genotypes under salinity stress.Functional & integrative genomics · 2016Article
- Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries, promoter sequence and gene expression analysis.Molecular genetics and genomics : MGG · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Endogenously-encoded microRNAs (miRNAs) are a class of small regulatory RNAs that modulate gene expression at the post-transcriptional level. In plants, miRNAs have increasingly been identified by experiments based on next-generation sequencing (NGS). However, promoter organization is currently unknown for most plant miRNAs, which are transcribed by RNA polymerase II. This deficiency prevents a comprehensive understanding of miRNA-mediated gene networks. In this study, by analyzing full-length cDNA sequences related to miRNAs, we mapped transcription start sites (TSSs) for 62 and 55 miRNAs in Arabidopsis and rice, respectively. The average free energy (AFE) profiles in the vicinity of TSSs were studied for both species. By employing position weight matrices (PWM) for 99 plant cis-elements, we discovered that three cis-elements were over-represented in the miRNA promoters of both species, while four and ten cis-elements were over-represented in Arabidopsis only and in rice only. Thus, comparison of miRNA promoters between Arabidopsis and rice provides a new perspective for studying miRNA regulation in plants.
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