ArticlePloS one2020
Poly(A)-seq: A method for direct sequencing and analysis of the transcriptomic poly(A)-tails.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Integrative analysis of Poly(A)-seq and RNA-seq reveals transcriptional regulation of poly(A) tail length in tuberculosis.Microbiology spectrum · 2026Article
- The bladder cancer mEMBO reports · 2026Article
- Controlling In Vitro mRNA Polyadenylation by Monitoring Poly(A) Polymerase Consumption of ATP.International journal of molecular sciences · 2026Article
- Dynamic regulation of mRNA acetylation at synapses by spatial memory in mouse hippocampus.eLife · 2026Article
- A kingdom-wide full-length RNA atlas reveals the evolutionary landscapes of plant poly(A) tails.Genome biology · 2026Article
- Pan2-Pan3 Complex-Mediated Deadenylation Enforces mRNA Quality Control for Infection of the Rice Blast Fungus.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Immune Responses to Influenza Infection in Children.Open forum infectious diseases · 2026Article
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.Communications biology · 2025Article
- An mRNA vaccine candidate encoding cholera toxin subunit B and conserved antigens of influenza viruses confers cross-protection against influenza a viruses in adult and aged mice.Human vaccines & immunotherapeutics · 2025Article
- Poly(A) tail regulation in stem cells and early development.Cell regeneration (London, England) · 2025Review
- Phosphorylation of CPR5 by the receptor-like kinase FLR2 promotes mRNA poly(A) tail processing and immunity to Magnaporthe oryzae in rice.Plant communications · 2025Article
- Endonucleolytic cleavage is the primary mechanism of decay elicited byGenome research · 2025Article
- RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation.BMC biology · 2025Article
- Current Analytical Strategies for mRNA-Based Therapeutics.Molecules (Basel, Switzerland) · 2025Review
- Recent advances in investigation of circRNA/lncRNA-miRNA-mRNA networks through RNA sequencing data analysis.Briefings in functional genomics · 2025Review
- Characterization of poly(A) and poly(T) tail lengths in plasmid DNA by liquid chromatography high-resolution mass spectrometry.Analytical and bioanalytical chemistry · 2025Article
- Thousands of oscillating LncRNAs in the mouse testis.Computational and structural biotechnology journal · 2024Article
- Sequencing of Transcriptome-Wide Poly(A) Tails by PAIso-seq.Methods in molecular biology (Clifton, N.J.) · 2024Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Poly(A) tails at the 3' end of eukaryotic messenger RNAs control mRNA stability and translation efficiency. Facilitated by various NGS methods, alternative polyadenylation sites determining the 3'-UTR length of gene transcripts have been extensively studied. However, poly(A) lengths demonstrating dynamic and developmental regulation remain largely unexplored. The recently developed NGS-based methods for genome-wide poly(A) profiling have promoted the study of genom-wide poly(A) dynamics. Here we present a straight forward NGS-method for poly(A) profiling, which applies a direct 3'-end adaptor ligation and the template switching for 5'-end adaptor ligation for cDNA library construction. Poly(A) lengths are directly calculated from base call data using a self-developed pipeline pA-finder. The libraries were directly sequenced from the 3'-UTR regions into the followed poly(A) tails, firstly on NextSeq 500 to produce single-end 300-nt reads, demonstrating the method feasibility and that optimization of the fragmented RNA size for cDNA library construction could detecting longer poly (A) tails. We next applied Poly(A)-seq cDNA libraries containing 40-nt and 120-nt poly(A) tail spike-in RNAs on HiSeq X-ten and NovaSeq 6000 to obtain 150-nt and 250-nt pair-end reads. The sequencing profiles of the spike-in RNAs demonstrated both high accuracy and high quality score in reading poly(A) tails. The poly(A) signal bleeding into the 3' adaptor sequence and a sharp decreased quality score at the junction were observed, allowing the modification of pA-finder to remove homopolymeric signal bleeding. We hope that wide applications of Poly(A)-seq help facilitate the study of the development- and disease-related poly(A) dynamics and regulation, and of the recent emerging mixed tailing regulation.
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