SynthesisNucleic acids research2009
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications.
Synthesis in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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.
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Who cites it
120 citing papers in PubMed, 1 synthesis or guideline pooled it, 203 citations in OpenAlex.
- A meta-analysis revealed insights into the sources, conservation and impact of microRNA 5'-isoforms in four model species.Nucleic acids research · 2014Pooled it
- Remodeling of tRNA modification in Trypanosoma cruzi life forms.PLoS pathogens · 2026Article
- Comparative analyses suggest a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants.BMC plant biology · 2024Article
- Terminal modifications independent cell-free RNA sequencing enables sensitive early cancer detection and classification.Nature communications · 2024Article
- Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing.Nature biotechnology · 2024Article
- One locus, several functional RNAs-emerging roles of the mechanisms responsible for the sequence variability of microRNAs.Biologia futura · 2023Review
- Seqpac: a framework for sRNA-seq analysis in R using sequence-based counts.Bioinformatics (Oxford, England) · 2023Article
- tRNA derived small RNAs-Small players with big roles.Frontiers in genetics · 2022Review
- A Novel Tissue Atlas and Online Tool for the Interrogation of Small RNA Expression in Human Tissues and Biofluids.Frontiers in cell and developmental biology · 2022Article
- Expression characteristics and interaction networks of microRNAs in spleen tissues of grass carp (Ctenopharyngodon idella).PloS one · 2022Article
- Aberration-corrected ultrafine analysis of miRNA reads at single-base resolution: a k-mer lattice approach.Nucleic acids research · 2021Article
- Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements.Biology · 2021Review
- Article
- Changes of the tRNA Modification Pattern during the Development ofNon-coding RNA · 2021Article
- High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq.Molecular cell · 2021Article
- Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification.RNA biology · 2021Article
- The MicroRNA Family Gets Wider: The IsomiRs Classification and Role.Frontiers in cell and developmental biology · 2021Review
- Methodologies for Transcript Profiling Using Long-Read Technologies.Frontiers in genetics · 2020Review
- Computational tools for plant small RNA detection and categorization.Briefings in bioinformatics · 2019Review
- Identification of tRNA-Derived Fragments Expression Profile in Breast Cancer Tissues.Current genomics · 2019Article
60 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
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in DNA-sequencing technology have made it possible to obtain large datasets of small RNA sequences. Here we demonstrate that not all non-perfectly matched small RNA sequences are simple technological sequencing errors, but many hold valuable biological information. Analysis of three small RNA datasets originating from Oryza sativa and Arabidopsis thaliana small RNA-sequencing projects demonstrates that many single nucleotide substitution errors overlap when aligning homologous non-identical small RNA sequences. Investigating the sites and identities of substitution errors reveal that many potentially originate as a result of post-transcriptional modifications or RNA editing. Modifications include N1-methyl modified purine nucleotides in tRNA, potential deamination or base substitutions in micro RNAs, 3' micro RNA uridine extensions and 5' micro RNA deletions. Additionally, further analysis of large sequencing datasets reveal that the combined effects of 5' deletions and 3' uridine extensions can alter the specificity by which micro RNAs associate with different Argonaute proteins. Hence, we demonstrate that not all sequencing errors in small RNA datasets are technical artifacts, but that these actually often reveal valuable biological insights to the sites of post-transcriptional RNA modifications.
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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.