Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila

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Cell Reports
We analyzed the usage and consequences of alternative cleavage and polyadenylation (APA) in $\textit{Drosophila melanogaster}$ by using >1 billion reads of stranded mRNA-seq across a variety of dissected tissues. Beyond demonstrating that a majority of fly transcripts are subject to APA, we observed broad trends for 3′ untranslated region (UTR) shortening in the testis and lengthening in the central nervous system (CNS); the latter included hundreds of unannotated extensions ranging up to 18 kb. Extensive northern analyses validated the accumulation of full-length neural extended transcripts, and in situ hybridization indicated their spatial restriction to the CNS. Genes encoding RNA binding proteins (RBPs) and transcription factors were preferentially subject to 3′ UTR extensions. Motif analysis indicated enrichment of miRNA and RBP sites in the neural extensions, and their termini were enriched in canonical cis elements that promote cleavage and polyadenylation. Altogether, we reveal broad tissue-specific patterns of APA in $\textit{Drosophila}$ and transcripts with unprecedented 3′ UTR length in the nervous system.
microRNA, RNA binding protein, 3' untranslated region, alternative cleavage and polyadenylation, binding site, Drosophila melanogaster, gene expression, in situ hybridization, nonhuman, Northern blotting, polyadenylation, protein motif, RNA sequence, tissue specificity, transcription regulation, Animals, Base Sequence, Blotting, Northern, Conserved Sequence, DNA-Binding Proteins, Drosophila melanogaster, Embryo, Nonmammalian, Gene Expression Regulation, Developmental, Genes, Insect, male, Molecular Sequence Data, Neurons, Nucleotide Motifs, Organ Specificity, Poly A, polyadenylation, Protein Isoforms, Reproducibility of Results, RNA, Messenger, Sequence Analysis, RNA, Testis, Transcriptome
Smibert, P., Miura, P., Westholm, J. O., Shenker, S., May, G., Duff, M. O., . . . Lai, E. C. (2012). Global patterns of tissue-specific alternative polyadenylation in drosophila. Cell Reports, 1(3), 277-289.
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© 2012 The Authors