ArticleNature communications2024
Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Leveraging long read RNA-seq to decipher neuronal regulation of alternative polyadenylation.Nature communications · 2026Article
- Alternative Polyadenylation in the Brain is Modulated by Chronic Ethanol Exposure in a Sex- and Cell Type-Specific Manner.Molecular neurobiology · 2026Article
- Article
- PASSpedia: A Polyadenylation Site Database Across Different Species at Single-cell Resolution.Genomics, proteomics & bioinformatics · 2026Article
- Post-transcriptional regulatory networks: The dynamic interplay of RNA-binding proteins.The FEBS journal · 2026Review
- Benchmarking computational methods for identifying and quantifying polyadenylation sites from 3' tag-based single-cell RNA-seq data.Nucleic acids research · 2026Article
- Regulation of gene expression by alternative polyadenylation in health and disease.Nature reviews. Genetics · 2026Review
- Mapping glioblastoma's isoform diversity using long-read single-cell analysis.Nature communications · 2026Article
- 3'UTR variants of ALS-linked RNAs modify subcellular and cellular phenotypes.The FEBS journal · 2026Article
- miRNA regulation in brain tissue space: the 3'UTR perspective.RNA (New York, N.Y.) · 2026Review
- Alternative polyadenylation links RNA processing to iron metabolism in human erythropoiesis.Nucleic acids research · 2026Article
- Intronic polyadenylation-derived long noncoding RNA modulates nucleolar integrity and function.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Differentiation in the human urothelia is defined by distinct alternative polyadenylation.Cell reports · 2026Article
- Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.Lipids in health and disease · 2026Article
- Targeting CPSF73, the mRNA 3' end processing endonuclease, moves cancer cells away from the mesenchymal state.Frontiers in immunology · 2026Article
- Single-nucleus transcriptome atlas of orbitofrontal cortex in ALS with a deep learning-based decoding of alternative polyadenylation mechanisms.Cell genomics · 2025Article
- Integrative analysis of RNA binding proteins identifies DDX55 as a novel regulator of 3'UTR isoform diversity.Genome biology · 2025Article
- scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data.Genome biology · 2025Article
- Quantification of transcript isoforms at the single-cell level using SCALPEL.Nature communications · 2025Article
- The quantitative impact of 3'UTRs on gene expression.Nucleic acids research · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Although more than half of all genes generate transcripts that differ in 3'UTR length, current analysis pipelines only quantify the amount but not the length of mRNA transcripts. 3'UTR length is determined by 3' end cleavage sites (CS). We map CS in more than 200 primary human and mouse cell types and increase CS annotations relative to the GENCODE database by 40%. Approximately half of all CS are used in few cell types, revealing that most genes only have one or two major 3' ends. We incorporate the CS annotations into a computational pipeline, called scUTRquant, for rapid, accurate, and simultaneous quantification of gene and 3'UTR isoform expression from single-cell RNA sequencing (scRNA-seq) data. When applying scUTRquant to data from 474 cell types and 2134 perturbations, we discover extensive 3'UTR length changes across cell types that are as widespread and coordinately regulated as gene expression changes but affect mostly different genes. Our data indicate that mRNA abundance and mRNA length are two largely independent axes of gene regulation that together determine the amount and spatial organization of protein synthesis.
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