ArticleBMC genomics2018
Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops.
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 10 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
10 citing papers in PubMed, 21 citations in OpenAlex.
- Decoding plant responses to waterlogging: from stress signals to molecular mechanisms and their future implications.Plant molecular biology · 2025Review
- Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses.Nature communications · 2023Article
- Responses of sorghum to cold stress: A review focused on molecular breeding.Frontiers in plant science · 2023Review
- The identification of conserved sequence features of co-translationally decayed mRNAs and upstream open reading frames in angiosperm transcriptomes.Plant direct · 2023Article
- RNA-Seq Reveals Waterlogging-Triggered Root Plasticity in Mungbean Associated with Ethylene and Jasmonic Acid Signal Integrators for Root Regeneration.Plants (Basel, Switzerland) · 2022Article
- Pan-Genome miRNomics inPlants (Basel, Switzerland) · 2021Article
- Comparative Analysis of Transcriptome and sRNAs Expression Patterns in theInternational journal of molecular sciences · 2021Article
- Monitoring of XRN4 Targets Reveals the Importance of Cotranslational Decay during Arabidopsis Development.Plant physiology · 2020Article
- Current breeding and genomic approaches to enhance the cane and sugar productivity under abiotic stress conditions.3 Biotech · 2020Review
- Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects.Frontiers in plant science · 2019Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundSince the proposal of Brachypodium distachyon as a model for the grasses, over 500 Bdi-miRNAs have been annotated in miRBase making Brachypodium second in number only to rice. Other monocots, such as switchgrass, are completely absent from the miRBase database. While a significant number of miRNAs have been identified which are highly conserved across plants, little research has been done with respect to the conservation of miRNA targets. Plant responses to abiotic stresses are regulated by diverse pathways many of which involve miRNAs; however, it can be difficult to identify miRNA guided gene regulation when the miRNA is not the primary regulator of the target mRNA.
resultsTo investigate miRNA target conservation and stress response involvement, a set of PARE (Parallel Analysis of RNA Ends) libraries totaling over two billion reads was constructed and sequenced from Brachypodium, switchgrass, and sorghum representing the first report of RNA degradome data from the latter two species. Analysis of this data provided not only PARE evidence for miRNA guided cleavage of over 7000 predicted target mRNAs in Brachypodium, but also evidence for miRNA guided cleavage of over 1000 homologous transcripts in sorghum and switchgrass. A pipeline was constructed to compare RNA-seq and PARE data made from Brachypodium plants exposed to various abiotic stress conditions. This resulted in the identification of 44 miRNA targets which exhibit stress regulated cleavage. Time course experiments were performed to reveal the relationship between miR393ab, miR169a, miR394ab, and their respective targets throughout the first 36 h of the cold stress response in Brachypodium.
conclusionsKnowledge gained from this study provides considerable insight into the RNA degradomes and the breadth of miRNA target conservation among these three species. Additionally, associations of a number of miRNAs and target mRNAs with the stress responses have been revealed which could aid in the development of stress tolerant transgenic crops.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.