ArticleRNA (New York, N.Y.)2016
3'READS+, a sensitive and accurate method for 3' end sequencing of polyadenylated RNA.
Article in RNA (New York, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 82 citations in OpenAlex.
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- miRNA regulation in brain tissue space: the 3'UTR perspective.RNA (New York, N.Y.) · 2026Review
- PolyA_DB v4: systematic polyA site identification and isoform annotation in human and mouse genomes using 3' end and long-read sequencing data.Nucleic acids research · 2026Article
- PeakPrime: a peak-guided primer design pipeline for target enrichment in 3'-end RNA-seq.Bioinformatics advances · 2026Article
- G-quadruplexes in the proximity 3'-UTR enhances alternative polyadenylation of Neogenin 1.iScience · 2025Article
- Light regulates widespread plant alternative polyadenylation through the chloroplast.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.RNA (New York, N.Y.) · 2023Review
- Deep learning of human polyadenylation sites at nucleotide resolution reveals molecular determinants of site usage and relevance in disease.Nature communications · 2023Article
- Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation.NAR genomics and bioinformatics · 2023Article
- The androgen receptor couples promoter recruitment of RNA processing factors to regulation of alternative polyadenylation at the 3' end of transcripts.Nucleic acids research · 2022Article
- CRISPRpas: programmable regulation of alternative polyadenylation by dCas9.Nucleic acids research · 2022Article
- CRISPR-iPAS: a novel dCAS13-based method for alternative polyadenylation interference.Nucleic acids research · 2022Article
- Article
- Neuronal Cells Display Distinct Stability Controls of Alternative Polyadenylation mRNA Isoforms, Long Non-Coding RNAs, and Mitochondrial RNAs.Frontiers in genetics · 2022Article
- TheProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Alternative 3' UTRs play a widespread role in translation-independent mRNA association with the endoplasmic reticulum.Cell reports · 2021Article
- LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival.BMC genomics · 2021Article
- The Detection and Bioinformatic Analysis of Alternative 3International journal of molecular sciences · 2021Review
- Streamlining differential exon and 3' UTR usage with diffUTR.BMC bioinformatics · 2021Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Sequencing of the 3' end of poly(A)(+) RNA identifies cleavage and polyadenylation sites (pAs) and measures transcript expression. We previously developed a method, 3' region extraction and deep sequencing (3'READS), to address mispriming issues that often plague 3' end sequencing. Here we report a new version, named 3'READS+, which has vastly improved accuracy and sensitivity. Using a special locked nucleic acid oligo to capture poly(A)(+) RNA and to remove the bulk of the poly(A) tail, 3'READS+ generates RNA fragments with an optimal number of terminal A's that balance data quality and detection of genuine pAs. With improved RNA ligation steps for efficiency, the method shows much higher sensitivity (over two orders of magnitude) compared to the previous version. Using 3'READS+, we have uncovered a sizable fraction of previously overlooked pAs located next to or within a stretch of adenylate residues in human genes and more accurately assessed the frequency of alternative cleavage and polyadenylation (APA) in HeLa cells (∼50%). 3'READS+ will be a useful tool to accurately study APA and to analyze gene expression by 3' end counting, especially when the amount of input total RNA is limited.
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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.