ArticleRNA biology2021
Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification.
Article in RNA biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 38 citations in OpenAlex.
- Reshaping organellar translation and tRNA metabolism: the consequences of photosynthesis loss and massive horizontal gene transfer.Molecular biology and evolution · 2026Article
- Tric proteins and TOM complex subunits are involved in the import of short DNA fragments into Arabidopsis mitochondria.Protoplasma · 2025Article
- Translational Regulation of Plant Stress Responses: Mechanisms, Pathways, and Applications in Bioengineering.Annual review of phytopathology · 2025Review
- Nanopore sequencing of intact aminoacylated tRNAs.Nature communications · 2025Article
- Fungal-Derived tRNAs Are Expressed and Aminoacylated in Orchid Mitochondria.Molecular biology and evolution · 2025Article
- The landscape of Arabidopsis tRNA aminoacylation.The Plant journal : for cell and molecular biology · 2024Article
- Experimental approaches to studying translation in plant semi-autonomous organelles.Journal of experimental botany · 2024Review
- Article
- Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pseudomonas fluorescens SBW25.Nucleic acids research · 2024Article
- A robust method for measuring aminoacylation through tRNA-Seq.bioRxiv : the preprint server for biology · 2024Article
- Advances in methods for tRNA sequencing and quantification.Trends in genetics : TIG · 2024Review
- tRNA gene content, structure, and organization in the flowering plant lineage.Frontiers in plant science · 2024Article
- A Preliminary Survey of Transfer RNA Modifications and Modifying Enzymes of the Tropical PlantGenes · 2023Article
- ALL-tRNAseq enables robust tRNA profiling in tissue samples.Genes & development · 2023Article
- Data-Independent Acquisition for the Detection of Mononucleoside RNA Modifications by Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2022Article
- Immunoprecipation Assay to Quantify the Amount of tRNAs associated with Their Interacting Proteins in Tissue and Cell Culture.Bio-protocol · 2022Article
- PltRNAdb: Plant transfer RNA database.PloS one · 2022Article
- Rapid Shifts in Mitochondrial tRNA Import in a Plant Lineage with Extensive Mitochondrial tRNA Gene Loss.Molecular biology and evolution · 2021Article
- Advances in Non-Coding RNA Sequencing.Non-coding RNA · 2021Review
- Targeted genome editing of plants and plant cells for biomanufacturing.Transgenic research · 2021Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in
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