ArticleGenome research2012
Dynamic landscape of tandem 3' UTRs during zebrafish development.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
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- Sex-specific transcriptome dynamics ofGenes & development · 2025Article
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- U1 snRNP proteins promote proximal alternative polyadenylation sites by directly interacting with 3' end processing core factors.Journal of molecular cell biology · 2022Article
- Nuclear mEMBO reports · 2022Article
- Dynamic and widespread control of poly(A) tail length during macrophage activation.RNA (New York, N.Y.) · 2022Article
- Inferring protein expression changes from mRNA in Alzheimer's dementia using deep neural networks.Nature communications · 2022Article
- Temporal Dynamic Analysis of Alternative Splicing During Embryonic Development in Zebrafish.Frontiers in cell and developmental biology · 2022Article
- Profiling of alternative polyadenylation and gene expression in PEDV-infected IPEC-J2 cells.Virus genes · 2021Article
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- PlantAPAdb: A Comprehensive Database for Alternative Polyadenylation Sites in Plants.Plant physiology · 2020Article
- Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis.BMC genomics · 2019Article
- Article
- Crosstalk between alternative polyadenylation and miRNAs in the regulation of protein translational efficiency.Genome research · 2018Article
- Differential genome-wide profiling of alternative polyadenylation sites in nasopharyngeal carcinoma by high-throughput sequencing.Journal of biomedical science · 2018Article
- Alternative Polyadenylation of Mammalian Transcripts Is Generally Deleterious, Not Adaptive.Cell systems · 2018Article
- Cell Cycle Regulation by Alternative Polyadenylation of CCND1.Scientific reports · 2018Article
- Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline.Genome biology · 2018Article
- Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events.Molecular biology and evolution · 2017Article
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tandem 3' untranslated regions (UTRs), produced by alternative polyadenylation (APA) in the terminal exon of a gene, could have critical roles in regulating gene networks. Here we profiled tandem poly(A) events on a genome-wide scale during the embryonic development of zebrafish (Danio rerio) using a recently developed SAPAS method. We showed that 43% of the expressed protein-coding genes have tandem 3' UTRs. The average 3' UTR length follows a V-shaped dynamic pattern during early embryogenesis, in which the 3' UTRs are first shortened at zygotic genome activation, and then quickly lengthened during gastrulation. Over 4000 genes are found to switch tandem APA sites, and the distinct functional roles of these genes are indicated by Gene Ontology analysis. Three families of cis-elements, including miR-430 seed, U-rich element, and canonical poly(A) signal, are enriched in 3' UTR-shortened/lengthened genes in a stage-specific manner, suggesting temporal regulation coordinated by APA and trans-acting factors. Our results highlight the regulatory role of tandem 3' UTR control in early embryogenesis and suggest that APA may represent a new epigenetic paradigm of physiological regulations.
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