ArticleNucleic acids research2019
Bias-minimized quantification of microRNA reveals widespread alternative processing and 3' end modification.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed, 118 citations in OpenAlex.
- RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols.Nucleic acids research · 2026Article
- The Hidden Layer of MicroRNA Regulation in Gynecologic Cancers: IsomiRs, Arm Switching, and RNA Epitranscriptomic Modifications.International journal of molecular sciences · 2026Review
- Protocol using AGO-APP for isolation and sequencing of argonaute-bound miRNAs in specific neuronal subtypes of the mouse brain.STAR protocols · 2026Article
- CLASHub is an integrated database and analytical platform for microRNA-target interactions.Nature communications · 2026Article
- Pilot study of dual-arm absolute quantification of miR-130a and miR-365a in plasma and urine reveals 3p/5p strand-ratio shifts in prostate cancer.Scientific reports · 2026Article
- An absolute quantification atlas of small non-coding RNAs across diverse mammalian tissues and cell lines.Nature communications · 2026Article
- In vivo AGO-APP for cell-type- and compartment-specific miRNA profiling in the mouse brain.Cell reports methods · 2026Article
- An intrinsically disordered region of Drosha selectively promotes miRNA biogenesis independent of tissue-specific Microprocessor condensates.Genes & development · 2026Article
- shRNAI: A deep neural network for the design of highly potent shRNAs.Molecular therapy. Nucleic acids · 2025Article
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- An endogenous cluster of target-directed microRNA degradation sites induces decay of distinct microRNA families.Cell reports · 2025Article
- MicroRNA-responsive ON-OFF hybrid mRNA switch for precise protein expression control.Molecular therapy. Nucleic acids · 2025Article
- Absolute quantification of mammalian microRNAs for therapeutic RNA cleavage and detargeting.RNA (New York, N.Y.) · 2025Article
- Translation suppresses exogenous target RNA-mediated microRNA decay.Nature communications · 2025Article
- A general RNA-templated RNA extension activity ofRNA (New York, N.Y.) · 2025Article
- Analysis of Processing, Post-Maturation, and By-Products of shRNA in Gene and Cell Therapy Applications.Methods and protocols · 2025Article
- The biogenesis and regulation of animal microRNAs.Nature reviews. Molecular cell biology · 2025Review
- In vivo AGO-APP identifies a module of microRNAs cooperatively preserving neural progenitors.PLoS genetics · 2025Article
- DragonRNA: Generality of DNA-primed RNA-extension activities by DNA-directed RNA polymerases.Nucleic acids research · 2025Article
- MicroRNA-874-3p is a Potential Contributor to Primary Hyperparathyroidism-Induced Osteoporosis.Clinical interventions in aging · 2025Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNAs (miRNAs) modulate diverse biological and pathological processes via post-transcriptional gene silencing. High-throughput small RNA sequencing (sRNA-seq) has been widely adopted to investigate the functions and regulatory mechanisms of miRNAs. However, accurate quantification of miRNAs has been limited owing to the severe ligation bias in conventional sRNA-seq methods. Here, we quantify miRNAs and their variants (known as isomiRs) by an improved sRNA-seq protocol, termed AQ-seq (accurate quantification by sequencing), that utilizes adapters with terminal degenerate sequences and a high concentration of polyethylene glycol (PEG), which minimize the ligation bias during library preparation. Measurement using AQ-seq allows us to correct the previously misannotated 5' end usage and strand preference in public databases. Importantly, the analysis of 5' terminal heterogeneity reveals widespread alternative processing events which have been underestimated. We also identify highly uridylated miRNAs originating from the 3p strands, indicating regulations mediated by terminal uridylyl transferases at the pre-miRNA stage. Taken together, our study reveals the complexity of the miRNA isoform landscape, allowing us to refine miRNA annotation and to advance our understanding of miRNA regulation. Furthermore, AQ-seq can be adopted to improve other ligation-based sequencing methods including crosslinking-immunoprecipitation-sequencing (CLIP-seq) and ribosome profiling (Ribo-seq).
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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.