ArticlePlant methods2022
A custom library construction method for super-resolution ribosome profiling in Arabidopsis.
Article in Plant methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 12 citations in OpenAlex.
- Stem cell activity is linked to a transient acquisition of pluripotency during callus proliferation.Nature communications · 2026Article
- Identifying and Visualizing Novel Small Open Reading Frames (sORFs) Via Ribo-Seq, Transcriptome Assembly, and ggRibo.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma's information flow.Genome biology · 2025Article
- Experimental approaches to studying translation in plant semi-autonomous organelles.Journal of experimental botany · 2024Review
- Ribosome Profiling and RNA Sequencing Reveal Translation and Transcription Regulation under Acute Heat Stress in Rainbow Trout (International journal of molecular sciences · 2024Article
- Frontiers in plant RNA research in ICAR2023: from lab to innovative agriculture.Plant molecular biology · 2024Article
- Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis.The Plant cell · 2024Article
- Protocol to measure ribosome density along mRNA transcripts of Arabidopsis thaliana tissues using Ribo-seq.STAR protocols · 2023Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundRibosome profiling, also known as Ribo-seq, is a powerful technique to study genome-wide mRNA translation. It reveals the precise positions and quantification of ribosomes on mRNAs through deep sequencing of ribosome footprints. We previously optimized the resolution of this technique in plants. However, several key reagents in our original method have been discontinued, and thus, there is an urgent need to establish an alternative protocol.
resultsHere we describe a step-by-step protocol that combines our optimized ribosome footprinting in plants with available custom library construction methods established in yeast and bacteria. We tested this protocol in 7-day-old Arabidopsis seedlings and evaluated the quality of the sequencing data regarding ribosome footprint length, mapped genomic features, and the periodic properties corresponding to actively translating ribosomes through open resource bioinformatic tools. We successfully generated high-quality Ribo-seq data comparable with our original method.
conclusionsWe established a custom library construction method for super-resolution Ribo-seq in Arabidopsis. The experimental protocol and bioinformatic pipeline should be readily applicable to other plant tissues and species.
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