ArticleMolecular systems biology2015
Single-cell polyadenylation site mapping reveals 3' isoform choice variability.
Article in Molecular systems biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Alternative cleavage and polyadenylation: key regulatory mechanisms in health and disease.RNA biology · 2025Review
- Dynamics of alternative polyadenylation in single root cells ofFrontiers in plant science · 2024Article
- Comprehensive mapping of alternative polyadenylation site usage and its dynamics at single-cell resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa.Plant physiology · 2022Article
- scAPAmod: Profiling Alternative Polyadenylation Modalities in Single Cells from Single-Cell RNA-Seq Data.International journal of molecular sciences · 2022Article
- Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression.Genome research · 2021Article
- The Detection and Bioinformatic Analysis of Alternative 3International journal of molecular sciences · 2021Review
- Computing the Role of Alternative Splicing in Cancer.Trends in cancer · 2021Review
- Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity.Nature communications · 2021Article
- Alternative Polyadenylation: a new frontier in post transcriptional regulation.Biomarker research · 2020Review
- Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation.Nature communications · 2020Article
- Article
- Gene expression dynamics are a proxy for selective pressures on alternatively polyadenylated isoforms.Nucleic acids research · 2020Article
- Targeted Perturb-seq enables genome-scale genetic screens in single cells.Nature methods · 2020Article
- Robust mapping of polyadenylated and non-polyadenylated RNA 3' ends at nucleotide resolution by 3'-end sequencing.Methods (San Diego, Calif.) · 2020Article
- Obstacles to detecting isoforms using full-length scRNA-seq data.Genome biology · 2020Article
- Understanding the complexity of retina and pluripotent stem cell derived retinal organoids with single cell RNA sequencing: current progress, remaining challenges and future prospective.Current eye research · 2020Review
- scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data.Bioinformatics (Oxford, England) · 2020Article
- Discovery of alternative polyadenylation dynamics from single cell types.Computational and structural biotechnology journal · 2020Review
- Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data.Nucleic acids research · 2019Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell-to-cell variability in gene expression is important for many processes in biology, including embryonic development and stem cell homeostasis. While heterogeneity of gene expression levels has been extensively studied, less attention has been paid to mRNA polyadenylation isoform choice. 3' untranslated regions regulate mRNA fate, and their choice is tightly controlled during development, but how 3' isoform usage varies within genetically and developmentally homogeneous cell populations has not been explored. Here, we perform genome-wide quantification of polyadenylation site usage in single mouse embryonic and neural stem cells using a novel single-cell transcriptomic method, BATSeq. By applying BATBayes, a statistical framework for analyzing single-cell isoform data, we find that while the developmental state of the cell globally determines isoform usage, single cells from the same state differ in the choice of isoforms. Notably this variation exceeds random selection with equal preference in all cells, a finding that was confirmed by RNA FISH data. Variability in 3' isoform choice has potential implications on functional cell-to-cell heterogeneity as well as utility in resolving cell populations.
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