ArticleGenome research2012
Extensive alternative polyadenylation 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 207 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
207 citing papers in PubMed, 343 citations in OpenAlex.
- The zebrafish model tackles anti-P2Y12 variability in humans: a translational approach.Blood advances · 2026Article
- LENG8 granule regulates alternative polyadenylation in mammals.Nature communications · 2026Article
- miR-133a-3p and miR-338-3p shape neural crest derivatives in zebrafish.Life science alliance · 2026Article
- PASSpedia: A Polyadenylation Site Database Across Different Species at Single-cell Resolution.Genomics, proteomics & bioinformatics · 2026Article
- Regulation of gene expression by alternative polyadenylation in health and disease.Nature reviews. Genetics · 2026Review
- Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans.PLoS biology · 2026Article
- Targeted blocking of gene splicing can dysregulate intron-embedded primary microRNAs.Communications biology · 2026Article
- MicroRNA-21 promotes dysregulated lipid metabolism and hepatocellular carcinoma.Disease models & mechanisms · 2026Article
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- A conserved 3'UTR short motif regulates gene expression in vertebrates.Nucleic acids research · 2026Article
- A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development.Genomics, proteomics & bioinformatics · 2025Article
- Alternative cleavage and polyadenylation: key regulatory mechanisms in health and disease.RNA biology · 2025Review
- High resolution of full-length RNA sequencing deciphers massive transcriptome complexity during zebrafish embryogenesis.BMC biology · 2025Article
- Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes.NAR genomics and bioinformatics · 2025Review
- The Dynamic Landscape of 3'-UTR Alternative Polyadenylation Across Mouse Fetal Development and Anatomy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus.Nature reviews. Genetics · 2025Review
- The CFII components PCF11 and Cbc change subnuclear localization as cells differentiate in an adult stem cell lineage.microPublication biology · 2025Article
- Alternative Splicing in the Heart: The Therapeutic Potential of Regulating the Regulators.International journal of molecular sciences · 2024Review
- Full-Length Transcriptome Profile ofInternational journal of molecular sciences · 2024Article
- Dynamic Alternative Polyadenylation duringGenes · 2024Article
147 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3' untranslated regions (3' UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-seq reads substantially increased and improved existing 3' UTR annotations, resulting in confidently identified 3' UTRs for >79% of the annotated protein-coding genes in zebrafish. mRNAs from most zebrafish genes undergo alternative CPA, with those from more than a thousand genes using different dominant 3' UTRs at different stages. These included one of the poly(A) polymerase genes, for which alternative CPA reinforces its repression in the ovary. 3' UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest 3' UTRs are highly expressed in the ovary, yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3' UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA. At 2 h post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3' UTRs provide a resource for studying gene regulation during vertebrate development.
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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.