Global patterns of tissue-specific alternative polyadenylation in Drosophila.
We analyzed the usage and consequences of alternative cleavage and polyadenylation (APA) in 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 Drosophila and transcripts with unprecedented 3' UTR length in the nervous system.
Department of Developmental Biology, Sloan-Kettering Institute, New York, NY 10065, USA.
Peter
P
Smibert
Pedro
P
Miura
Jakub O
JO
Westholm
Sol
S
Shenker
Gemma
G
May
Michael O
MO
Duff
Dayu
D
Zhang
Brian D
BD
Eads
Joe
J
Carlson
James B
JB
Brown
Robert C
RC
Eisman
Justen
J
Andrews
Thomas
T
Kaufman
Peter
P
Cherbas
Susan E
SE
Celniker
Brenton R
BR
Graveley
Eric C
EC
Lai
D020413:3' Untranslated Regions / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D015152:Blotting, Northern; D017124:Conserved Sequence / Q000235:genetics; D004268:DNA-Binding Proteins / Q000378:metabolism; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics*; D004625:Embryo, Nonmammalian / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D017344:Genes, Insect / Q000235:genetics; D017403:In Situ Hybridization; D008297:Male; D008969:Molecular Sequence Data; D009474:Neurons / Q000166:cytology / Q000378:metabolism; D059372:Nucleotide Motifs / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics*; D011061:Poly A / Q000378:metabolism; D026723:Polyadenylation / Q000235:genetics*; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D013737:Testis / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics
D020413:3' Untranslated Regions; D004268:DNA-Binding Proteins; D020033:Protein Isoforms; D012333:RNA, Messenger; D011061:Poly A