ArticleGenome biology2017
Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 69 citations in OpenAlex.
- LENG8 granule regulates alternative polyadenylation in mammals.Nature communications · 2026Article
- Article
- PASSpedia: A Polyadenylation Site Database Across Different Species at Single-cell Resolution.Genomics, proteomics & bioinformatics · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Polyadenylation Complex CFII Recognizes Downstream Cis-element for Pre-mRNA Polyadenylation Through Interaction with an RNA-Binding Protein in Arabidopsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Multitissue single-nucleus RNA-seq reveals cell type-specific regulatory patterns of alternative polyadenylation in pigs.Genome research · 2025Article
- Alternative Splicing and Alternative Polyadenylation-Regulated Cold Stress Response ofInsects · 2024Article
- Phylogenomic instructed target analysis reveals ELAV complex binding to multiple optimally spaced U-rich motifs.Nucleic acids research · 2024Article
- De Novo Genes.Annual review of genetics · 2024Review
- Rapid evolution of promoters from germline-specifically expressed genes including transposon silencing factors.BMC genomics · 2024Article
- Chromosome-Level Assembly and Annotation of the Pearly Heath Coenonympha arcania Butterfly Genome.Genome biology and evolution · 2024Article
- Genome-wide kinetic profiling of pre-mRNA 3' end cleavage.RNA (New York, N.Y.) · 2024Article
- Regulation of alternative splicing and polyadenylation in neurons.Life science alliance · 2023Review
- Article
- 3'UTR of mRNA Encoding CPEB Protein Orb2 Plays an Essential Role in Intracellular Transport in Neurons.Cells · 2023Article
- Regulatory logic of endogenous RNAi in silencing de novo genomic conflicts.PLoS genetics · 2023Article
- Distinct biogenesis pathways may have led to functional divergence of the human and Drosophila Arglu1 sisRNA.EMBO reports · 2023Article
- Long-Term Memory Formation inCells · 2023Article
- Regulation and function of alternative polyadenylation in development and differentiation.RNA biology · 2023Review
- Diverse cell-specific patterns of alternative polyadenylation in Drosophila.Nature communications · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundDrosophila melanogaster has one of best-described transcriptomes of any multicellular organism. Nevertheless, the paucity of 3'-sequencing data in this species precludes comprehensive assessment of alternative polyadenylation (APA), which is subject to broad tissue-specific control.
resultsHere, we generate deep 3'-sequencing data from 23 developmental stages, tissues, and cell lines of D. melanogaster, yielding a comprehensive atlas of ~ 62,000 polyadenylated ends. These data broadly extend the annotated transcriptome, identify ~ 40,000 novel 3' termini, and reveal that two-thirds of Drosophila genes are subject to APA. Furthermore, we dramatically expand the numbers of genes known to be subject to tissue-specific APA, such as 3' untranslated region (UTR) lengthening in head and 3' UTR shortening in testis, and characterize new tissue and developmental 3' UTR patterns. Our thorough 3' UTR annotations permit reassessment of post-transcriptional regulatory networks, via conserved miRNA and RNA binding protein sites. To evaluate the evolutionary conservation and divergence of APA patterns, we generate developmental and tissue-specific 3'-seq libraries from Drosophila yakuba and Drosophila virilis. We document broadly analogous tissue-specific APA trends in these species, but also observe significant alterations in 3' end usage across orthologs. We exploit the population of functionally evolving poly(A) sites to gain clear evidence that evolutionary divergence in core polyadenylation signal (PAS) and downstream sequence element (DSE) motifs drive broad alterations in 3' UTR isoform expression across the Drosophila phylogeny.
conclusionsThese data provide a critical resource for the Drosophila community and offer many insights into the complex control of alternative tissue-specific 3' UTR formation and its consequences for post-transcriptional regulatory networks.
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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.