ArticleQuantitative biology (Beijing, China)2018
Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data.
Article in Quantitative biology (Beijing, China), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 35 citations in OpenAlex.
- Single-cell profiling and genetic regulation of alternative polyadenylation in the human brain.Nature genetics · 2026Article
- Alternative Polyadenylation in the Brain is Modulated by Chronic Ethanol Exposure in a Sex- and Cell Type-Specific Manner.Molecular neurobiology · 2026Article
- Regulation of gene expression by alternative polyadenylation in health and disease.Nature reviews. Genetics · 2026Review
- Single-Cell Gene Module Inference Reveals Alternative Polyadenylation Dynamics Associated with Autism.International journal of molecular sciences · 2026Article
- A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development.Genomics, proteomics & bioinformatics · 2025Article
- Single-nucleus transcriptome atlas of orbitofrontal cortex in ALS with a deep learning-based decoding of alternative polyadenylation mechanisms.Cell genomics · 2025Article
- Quantification of transcript isoforms at the single-cell level using SCALPEL.Nature communications · 2025Article
- Article
- RNA-Binding Proteins: A Role in Neurotoxicity?Neurotoxicity research · 2023Review
- Extension of mRNA poly(A) tails and 3'UTRs during neuronal differentiation exhibits variable association with post-transcriptional dynamics.Nucleic acids research · 2023Article
- Article
- Emerging roles of alternative cleavage and polyadenylation (APA) in human disease.Journal of cellular physiology · 2022Review
- Neuronal Cells Display Distinct Stability Controls of Alternative Polyadenylation mRNA Isoforms, Long Non-Coding RNAs, and Mitochondrial RNAs.Frontiers in genetics · 2022Article
- Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data.Genome research · 2021Article
- Dynamic Variations of 3'UTR Length Reprogram the mRNA Regulatory Landscape.Biomedicines · 2021Review
- Alternative 3' UTRs play a widespread role in translation-independent mRNA association with the endoplasmic reticulum.Cell reports · 2021Article
- The Detection and Bioinformatic Analysis of Alternative 3International journal of molecular sciences · 2021Review
- A conserved role for the ALS-linked splicing factor SFPQ in repression of pathogenic cryptic last exons.Nature communications · 2021Article
- Animal-APAdb: a comprehensive animal alternative polyadenylation database.Nucleic acids research · 2021Article
- The Fine Art of Writing a Message: RNA Metabolism in the Shaping and Remodeling of the Nervous System.Frontiers in molecular neuroscience · 2021Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundMost eukaryotic protein-coding genes exhibit alternative cleavage and polyadenylation (APA), resulting in mRNA isoforms with different 3' untranslated regions (3' UTRs). Studies have shown that brain cells tend to express long 3' UTR isoforms using distal cleavage and polyadenylation sites (PASs).
methodsUsing our recently developed, comprehensive PAS database PolyA_DB, we developed an efficient method to examine APA, named Significance Analysis of Alternative Polyadenylation using RNA-seq (SAAP-RS). We applied this method to study APA in brain cells and neurogenesis.
resultsWe found that neurons globally express longer 3' UTRs than other cell types in brain, and microglia and endothelial cells express substantially shorter 3' UTRs. We show that the 3' UTR diversity across brain cells can be corroborated with single cell sequencing data. Further analysis of APA regulation of 3' UTRs during differentiation of embryonic stem cells into neurons indicates that a large fraction of the APA events regulated in neurogenesis are similarly modulated in myogenesis, but to a much greater extent.
conclusionTogether, our data delineate APA profiles in different brain cells and indicate that APA regulation in neurogenesis is largely an augmented process taking place in other types of cell 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.