ArticleeLife2025
Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR.
Article in eLife, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Dietary effects on cytosolic and mitochondrial tRNA abundance and modification patterns across mouse tissues.Genome research · 2026Article
- OTTR-CLASH: improved biochemical and bioinformatic identification of Argonaute 2-mediated microRNA-target RNA interactions.bioRxiv : the preprint server for biology · 2026Article
- OTTR-seq profiling reveals dynamic tRNA modification landscapes across diverse archaeal species.Genome biology · 2026Article
- FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling.Genome biology · 2026Article
- The regulation, function and disease relevance of cytoplasmic tRNAs.Nature reviews. Molecular cell biology · 2026Review
- tRNA-derived RNA processing in sperm transmits non-genetically inherited phenotypes to offspring in C. elegans.Nature communications · 2026Article
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
- An Improved Description of the Small RNA Landscape of the Human Fungal Pathogen Aspergillus fumigatus.Molecular microbiology · 2026Article
- Diverse expression and modification of tRNAs and tRNA-derived RNAs in 19 mouse tissues.bioRxiv : the preprint server for biology · 2025Article
- Pseudouridine selects RNAs for extracellular transport.bioRxiv : the preprint server for biology · 2025Article
- The Landscape of tRNA Modifications in Archaea.bioRxiv : the preprint server for biology · 2025Article
- Polyglycine-mediated aggregation of FAM98B disrupts tRNA processing in GGC repeat disorders.Science (New York, N.Y.) · 2025Article
- Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs.mBio · 2025Article
- Article
- Improved precision, sensitivity, and adaptability of ordered two-template relay cDNA library preparation for RNA sequencing.RNA (New York, N.Y.) · 2025Article
- Epididymis-specific RNase A family genes regulate fertility and small RNA processing.The Journal of biological chemistry · 2024Article
- Improved precision, sensitivity, and adaptability of Ordered Two-Template Relay cDNA library preparation for RNA sequencing.bioRxiv : the preprint server for biology · 2024Article
- A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3' termini.Molecular cell · 2024Article
- Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing.Nature biotechnology · 2024Article
- When Dad's Stress Gets under Kid's Skin-Impacts of Stress on Germline Cargo and Embryonic Development.Biomolecules · 2023Review
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Among the major classes of RNAs in the cell, tRNAs remain the most difficult to characterize via deep sequencing approaches, as tRNA structure and nucleotide modifications can each interfere with cDNA synthesis by commonly used reverse transcriptases (RTs). Here, we benchmark a recently developed RNA cloning protocol, termed Ordered Two-Template Relay (OTTR), to characterize intact tRNAs and tRNA fragments in budding yeast and in mouse tissues. We show that OTTR successfully captures both full-length tRNAs and tRNA fragments in budding yeast and in mouse reproductive tissues without any prior enzymatic treatment, and that tRNA cloning efficiency can be further enhanced via AlkB-mediated demethylation of modified nucleotides. As with other recent tRNA cloning protocols, we find that a subset of nucleotide modifications leave misincorporation signatures in OTTR datasets, enabling their detection without any additional protocol steps. Focusing on tRNA cleavage products, we compare OTTR with several standard small RNA-Seq protocols, finding that OTTR provides the most accurate picture of tRNA fragment levels by comparison to 'ground truth' Northern blots. Applying this protocol to mature mouse spermatozoa, our data dramatically alter our understanding of the small RNA cargo of mature mammalian sperm, revealing a far more complex population of tRNA fragments - including both 5' and 3' tRNA halves derived from the majority of tRNAs - than previously appreciated. Taken together, our data confirm the superior performance of OTTR to commercial protocols in analysis of tRNA fragments, and force a reappraisal of potential epigenetic functions of the sperm small RNA payload.
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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.