ArticleBMC genomics2021
LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 44 citations in OpenAlex.
- Temporal gating dictates stress-induced transcript export from the nucleus.Genes & development · 2026Article
- Subcellular localization of human long non-coding RNAs is an isoform-resolved property masked by gene-level analysis.Molecular genetics and genomics : MGG · 2026Article
- Leveraging long read RNA-seq to decipher neuronal regulation of alternative polyadenylation.Nature communications · 2026Article
- Construction of PANoptosis-related lncRNA prognostic model and immunotherapy sensitivity analysis in lung adenocarcinoma.Journal of cardiothoracic surgery · 2026Article
- Alternative 3' Polyadenylation Responses to Acute Ethanol Exposure Differ Between Drosophila Populations.Research square · 2026Article
- CRISPR/Cas9 screening with destabilized bicistronic fluorescent protein reporter revealed PABPN1 as a hub of regulators for alternative polyadenylation.Nucleic acids research · 2026Article
- 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
- mRNA initiation and termination are spatially coordinated.Science (New York, N.Y.) · 2025Article
- Multitissue single-nucleus RNA-seq reveals cell type-specific regulatory patterns of alternative polyadenylation in pigs.Genome research · 2025Article
- APALORD: An R-based tool for differential alternative polyadenylation analysis of long-read RNA-seq data.bioRxiv : the preprint server for biology · 2025Article
- Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.Molecular cell · 2024Article
- ThrScience advances · 2024Article
- Co-transcriptional gene regulation in eukaryotes and prokaryotes.Nature reviews. Molecular cell biology · 2024Review
- Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression.Nature communications · 2024Article
- Genome-scale requirements for dynein-based transport revealed by a high-content arrayed CRISPR screen.The Journal of cell biology · 2024Article
- InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data.Nature communications · 2024Article
- Genome-wide kinetic profiling of pre-mRNA 3' end cleavage.RNA (New York, N.Y.) · 2024Article
- Multiplexed screening reveals how cancer-specific alternative polyadenylation shapes tumor growth in vivo.Nature communications · 2024Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
backgroundThe sequence content of the 3' UTRs of many mRNA transcripts is regulated through alternative polyadenylation (APA). The study of this process using RNAseq data, though, has been historically challenging.
resultsTo combat this problem, we developed LABRAT, an APA isoform quantification method. LABRAT takes advantage of newly developed transcriptome quantification techniques to accurately determine relative APA site usage and how it varies across conditions. Using LABRAT, we found consistent relationships between gene-distal APA and subcellular RNA localization in multiple cell types. We also observed connections between transcription speed and APA site choice as well as tumor-specific transcriptome-wide shifts in APA isoform abundance in hundreds of patient-derived tumor samples that were associated with patient prognosis. We investigated the effects of APA on transcript expression and found a weak overall relationship, although many individual genes showed strong correlations between relative APA isoform abundance and overall gene expression. We interrogated the roles of 191 RNA-binding proteins in the regulation of APA isoforms, finding that dozens promote broad, directional shifts in relative APA isoform abundance both in vitro and in patient-derived samples. Finally, we find that APA site shifts in the two classes of APA, tandem UTRs and alternative last exons, are strongly correlated across many contexts, suggesting that they are coregulated.
conclusionsWe conclude that LABRAT has the ability to accurately quantify APA isoform ratios from RNAseq data across a variety of sample types. Further, LABRAT is able to derive biologically meaningful insights that connect APA isoform regulation to cellular and molecular phenotypes.
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