ArticleNature methods2013
Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing.
Article in Nature methods, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 314 papers.
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.
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Who cites it
314 citing papers in PubMed.
- Investigating the role of CpG islands and DNA methylation at 3'UTRs in cancer.Life science alliance · 2026Article
- Leveraging long read RNA-seq to decipher neuronal regulation of alternative polyadenylation.Nature communications · 2026Article
- Identification of specific transcripts for plant heat stress tolerance through genome-wide analysis of SIZ1-dependent alternative polyadenylation.Stress biology · 2026Article
- Mechanisms coordinating exit from the stem cell state in mammals.Genes & development · 2026Review
- PASSpedia: A Polyadenylation Site Database Across Different Species at Single-cell Resolution.Genomics, proteomics & bioinformatics · 2026Article
- Nucleotide resolution 4-thiouridine sequencing by SNU-Seq and sf4sU-Seq reveals the transcriptional responsiveness of an epigenetically primed human genome.Nucleic acids research · 2026Article
- APAdeg enhances differentially expressed gene inference by leveraging site-specific signals in APA-seq data.Briefings in bioinformatics · 2026Article
- Regulation of gene expression by alternative polyadenylation in health and disease.Nature reviews. Genetics · 2026Review
- Long Noncoding RNA Isoform Specificity and Chemical Modification on tRNA-Derived Fragments Leading to Divergent Functions.The American journal of pathology · 2026Review
- Alternative polyadenylation releases PCBP1-mediated suppression of CFIm25 during macrophage differentiation.FEBS letters · 2026Article
- Modulating the cleavage and polyadenylation site: from research tools to therapeutic opportunities.RNA (New York, N.Y.) · 2026Review
- miRNA regulation in brain tissue space: the 3'UTR perspective.RNA (New York, N.Y.) · 2026Review
- Full-length transcriptome atlas of porcine skeletal muscle reveals isoform-resolved genetic regulatory mechanisms for muscle growth.BMC genomics · 2026Article
- Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans.PLoS biology · 2026Article
- A practical guide to targeted single-cell RNA sequencing technologies.Communications biology · 2026Review
- 3'UTR shortening alleviates miRNA repression of mRNAs critical for muscle stem cell differentiation.The EMBO journal · 2026Article
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- Comprehensive mapping of the 5' and 3' untranslated regions ofRNA (New York, N.Y.) · 2026Article
- ASTWAS: modeling alternative polyadenylation and SNP effects in kernel-driven TWAS reveal novel genetic associations for complex traits.Briefings in bioinformatics · 2026Article
- 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
254 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Alternative cleavage and polyadenylation (APA) generates diverse mRNA isoforms. We developed 3' region extraction and deep sequencing (3'READS) to address mispriming issues that commonly plague poly(A) site (pA) identification, and we used the method to comprehensively map pAs in the mouse genome. Thorough annotation of gene 3' ends revealed over 5,000 previously overlooked pAs (∼8% of total) flanked by A-rich sequences, underscoring the necessity of using an accurate tool for pA mapping. About 79% of mRNA genes and 66% of long noncoding RNA genes undergo APA, but these two gene types have distinct usage patterns for pAs in introns and upstream exons. Quantitative analysis of APA isoforms by 3'READS indicated that promoter-distal pAs, regardless of intron or exon locations, become more abundant during embryonic development and cell differentiation and that upregulated isoforms have stronger pAs, suggesting global modulation of the 3' end-processing activity in development and differentiation.
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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.