ArticleGenome biology2021
Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 37 citations in OpenAlex.
- An ancient retrotransposon provides species-specific tuning of IL-18 inflammatory signaling.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking computational methods for identifying and quantifying polyadenylation sites from 3' tag-based single-cell RNA-seq data.Nucleic acids research · 2026Article
- Integrator subunit IntS11 orchestrates the temporal dynamics of neural lineage progression in Drosophila.Cell & bioscience · 2026Article
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development.Genomics, proteomics & bioinformatics · 2025Article
- Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3'UTR isoform diversity.Genome biology · 2025Article
- TDP-43 loss induces cryptic polyadenylation in ALS/FTD.Nature neuroscience · 2025Article
- Transition of CELF2 PAS usage promotes recovery of refractory JDM through alternative splicing regulation of CTSB.Molecular therapy. Nucleic acids · 2025Article
- Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes.NAR genomics and bioinformatics · 2025Review
- Selecting differential splicing methods: Practical considerations for short-read RNA sequencing.F1000Research · 2025Review
- Review
- Crosstalk among Alternative Polyadenylation, Genetic Variants and Ubiquitin Modification Contribute to Lung Adenocarcinoma Risk.International journal of molecular sciences · 2024Article
- Colocalization analysis of 3' UTR alternative polyadenylation quantitative trait loci reveals novel mechanisms underlying associations with lung function.Human molecular genetics · 2024Article
- InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data.Nature communications · 2024Article
- Article
- The implication of integrative multiple RNA modification-based subtypes in gastric cancer immunotherapy and prognosis.iScience · 2024Article
- Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella.Plant cell reports · 2024Article
- Polygenic risk for schizophrenia converges on alternative polyadenylation as molecular mechanism underlying synaptic impairment.bioRxiv : the preprint server for biology · 2024Article
- Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.RNA (New York, N.Y.) · 2023Review
- Current technical advancements in plant epitranscriptomic studies.The plant genome · 2023Review
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundAlternative cleavage and polyadenylation (APA), an RNA processing event, occurs in over 70% of human protein-coding genes. APA results in mRNA transcripts with distinct 3' ends. Most APA occurs within 3' UTRs, which harbor regulatory elements that can impact mRNA stability, translation, and localization.
resultsAPA can be profiled using a number of established computational tools that infer polyadenylation sites from standard, short-read RNA-seq datasets. Here, we benchmarked a number of such tools-TAPAS, QAPA, DaPars2, GETUTR, and APATrap- against 3'-Seq, a specialized RNA-seq protocol that enriches for reads at the 3' ends of genes, and Iso-Seq, a Pacific Biosciences (PacBio) single-molecule full-length RNA-seq method in their ability to identify polyadenylation sites and quantify polyadenylation site usage. We demonstrate that 3'-Seq and Iso-Seq are able to identify and quantify the usage of polyadenylation sites more reliably than computational tools that take short-read RNA-seq as input. However, we find that running one such tool, QAPA, with a set of polyadenylation site annotations derived from small quantities of 3'-Seq or Iso-Seq can reliably quantify variation in APA across conditions, such asacross genotypes, as demonstrated by the successful mapping of alternative polyadenylation quantitative trait loci (apaQTL).
conclusionsWe envisage that our analyses will shed light on the advantages of studying APA with more specialized sequencing protocols, such as 3'-Seq or Iso-Seq, and the limitations of studying APA with short-read RNA-seq. We provide a computational pipeline to aid in the identification of polyadenylation sites and quantification of polyadenylation site usages using Iso-Seq data as input.
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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.