ArticleNature methods2023
Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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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.
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Who cites it
49 citing papers in PubMed, 58 citations in OpenAlex.
- Review
- Folding the message: mRNA structure as a regulatory layer of human mitochondrial gene expression.Biochimica et biophysica acta. Molecular cell research · 2026Review
- Single-molecule mbioRxiv : the preprint server for biology · 2026Article
- VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.Nucleic acids research · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling.Genome biology · 2026Article
- An rRNA-depleted full-length transcriptome strategy using nanopore sequencing for identification of novel lncRNA isoforms.Communications biology · 2026Article
- TENT-5 polyadenylates and regulates male-specific transcripts in Caenorhabditis elegans.G3 (Bethesda, Md.) · 2026Article
- Pan-organ poly(A) atlas reveals a post-transcriptional regulatory layer independent of RNA abundance.Nature communications · 2026Article
- Mapping human pre-rRNA processing and modification at single nucleotide resolution using long read nanopore sequencing.Nature communications · 2026Article
- A dual context-aware basecaller for nanopore direct RNA sequencing.Nature communications · 2026Article
- The new era of single-molecule RNA modification detection through nanopore base-calling models.Nature reviews. Molecular cell biology · 2026Review
- Engineering the poly(A) tail for therapeutic mRNA: from expression control to manufacturing robustness.Frontiers in bioengineering and biotechnology · 2026Review
- Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.Communications biology · 2025Article
- Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution.Nature protocols · 2025Review
- Investigating RNA dynamics from single molecule transcriptomes.Trends in genetics : TIG · 2025Review
- Long-read sequencing-based analyses of the adult Drosophila brain transcriptome in physiological and pathological settings.BMC genomics · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- 3AIM-seq: Quality assessment of mRNA therapeutics using sequencing for 3' poly(A) tails of in vitro-transcribed mRNA.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos.Nucleic acids research · 2025Article
Corrections and comments
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Authors and funding
11 authors at 6 institutions in 4 countries.
Funding
Abstract
RNA polyadenylation plays a central role in RNA maturation, fate, and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore 3' end-capture sequencing (Nano3P-seq), a method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition, and tail length dynamics at per-read resolution. By employing a template-switching-based sequencing protocol, Nano3P-seq can sequence RNA molecule from its 3' end, regardless of its polyadenylation status, without the need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P-seq provides quantitative estimates of RNA abundance and tail lengths, and captures a wide diversity of RNA biotypes. We find that, in addition to mRNA and long non-coding RNA, polyA tails can be identified in 16S mitochondrial ribosomal RNA in both mouse and zebrafish models. Moreover, we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform-specific level, correlating with mRNA decay. Finally, we demonstrate the ability of Nano3P-seq in capturing non-A bases within polyA tails of various lengths, and reveal their distribution during vertebrate embryogenesis. Overall, Nano3P-seq is a simple and robust method for accurately estimating transcript levels, tail lengths, and tail composition heterogeneity in individual reads, with minimal library preparation biases, both in the coding and non-coding transcriptome.
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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.