ArticleNucleic acids research2015
The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
129 citing papers in PubMed.
- Dietary effects on cytosolic and mitochondrial tRNA abundance and modification patterns across mouse tissues.Genome research · 2026Article
- Mitochondrial tRNA-Derived Fragments as Candidate Metastasis-Modifying RNA.Cancer research communications · 2026Article
- FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling.Genome biology · 2026Article
- Article
- Article
- RNA Modifications in Health and Disease.MedComm · 2025Review
- Post-Transcriptional Modifications of the Large Ribosome Subunit Assembly Intermediates inBiochemistry · 2025Article
- A comparative evaluation of computational models for RNA modification detection using nanopore sequencing with RNA004 chemistry.Briefings in bioinformatics · 2025Article
- A Comparative Evaluation of Computational Models for RNA modification detection using Nanopore sequencing with RNA004 Chemistry.bioRxiv : the preprint server for biology · 2025Article
- Next-Generation Sequencing Methods to Determine the Accuracy of Retroviral Reverse Transcriptases: Advantages and Limitations.Viruses · 2025Review
- tRNA hypomodification facilitates 5-fluorocytosine resistance via cross-pathway control system activation in Aspergillus fumigatus.Nucleic acids research · 2025Article
- High-throughput detection of RNA modifications at single base resolution.FEBS letters · 2025Review
- The landscape of Arabidopsis tRNA aminoacylation.The Plant journal : for cell and molecular biology · 2024Article
- DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing.Nucleic acids research · 2024Article
- tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.Nucleic acids research · 2024Article
- Mass Spectrometry-Based Direct Sequencing of tRNAs De Novo and Quantitative Mapping of Multiple RNA Modifications.Journal of the American Chemical Society · 2024Article
- Comparative analyses suggest a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants.BMC plant biology · 2024Article
- Quantification of tRNA mRNA (New York, N.Y.) · 2024Article
- General Principles and Limitations for Detection of RNA Modifications by Sequencing.Accounts of chemical research · 2024Article
- Current technical advancements in plant epitranscriptomic studies.The plant genome · 2023Review
69 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA. Here we simultaneously analyze both parameters in detail with respect to the occurrence of N-1-methyladenosine (m(1)A) in the template RNA. This naturally occurring modification is associated with structural effects, but it is also known as a mediator of antibiotic resistance in ribosomal RNA. In structural probing experiments with dimethylsulfate, m(1)A is routinely detected by RT-arrest. A specifically developed RNA-Seq protocol was tailored to the simultaneous analysis of RT-arrest and misincorporation patterns. By application to a variety of native and synthetic RNA preparations, we found a characteristic signature of m(1)A, which, in addition to an arrest rate, features misincorporation as a significant component. Detailed analysis suggests that the signature depends on RNA structure and on the nature of the nucleotide 3' of m(1)A in the template RNA, meaning it is sequence dependent. The RT-signature of m(1)A was used for inspection and confirmation of suspected modification sites and resulted in the identification of hitherto unknown m(1)A residues in trypanosomal tRNA.
Indexed as
Identifiers
What OpenQuestion holds
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.