ArticleGenome biology2013
Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 76 citations in OpenAlex.
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- Parallel analysis of RNA ends reveals global microRNA-mediated target RNA cleavage in maize.The Plant journal : for cell and molecular biology · 2022Article
- TRUEE; a bioinformatic pipeline to define the functional microRNA targetome of Arabidopsis.The Plant journal : for cell and molecular biology · 2022Article
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- Posttranscriptional regulation of cellulose synthase genes by small RNAs derived from cellulose synthase antisense transcripts.Plant direct · 2021Article
- A novel plant-fungal association reveals fundamental sRNA and gene expression reprogramming at the onset of symbiosis.BMC biology · 2021Article
- Pan-Genome miRNomics inPlants (Basel, Switzerland) · 2021Article
- Small Non-Coding RNAs at the Crossroads of Regulatory Pathways Controlling Somatic Embryogenesis in Seed Plants.Plants (Basel, Switzerland) · 2021Review
- Comparative Analysis of Transcriptome and sRNAs Expression Patterns in theInternational journal of molecular sciences · 2021Article
- Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach.Frontiers in molecular biosciences · 2021Article
- Differential Expression of Maize and Teosinte microRNAs under Submergence, Drought, and Alternated Stress.Plants (Basel, Switzerland) · 2020Article
- Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts.International journal of molecular sciences · 2020Article
- Genome-wide analysis of brassinosteroid responsive small RNAs in Arabidopsis thaliana.Genes & genomics · 2020Article
- Evolution of PHAS loci in the young spike of Allohexaploid wheat.BMC genomics · 2020Article
- RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4.Nucleic acids research · 2019Article
- Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos.Scientific reports · 2019Article
- Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects.Frontiers in plant science · 2019Review
- Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops.BMC genomics · 2018Article
- Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity.International journal of molecular sciences · 2018Review
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Authors and funding
15 authors at 5 institutions in 1 country.
Funding
Abstract
backgroundThe wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using parallel analysis of RNA ends (PARE) data is lacking in B. distachyon.
resultsB. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants. To investigate miRNA-mediated cleavage function, four PARE libraries were constructed from key tissues and sequenced to a total depth of approximately 70 million sequences. The roughly 5 million distinct genome-matched sequences that resulted represent an extensive dataset for analyzing small RNA-guided cleavage events. Analysis of the PARE and miRNA data provided experimental evidence for miRNA-mediated cleavage of 264 sites in predicted miRNA targets. In addition, PARE analysis revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner.
conclusionsB. distachyon miRNAs and target RNAs were experimentally identified and analyzed. Knowledge gained from this study should provide insights into the roles of miRNAs and the regulation of their targets in B. distachyon and related plants.
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