title: Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster.
abstract: Analysis of EST and cDNA collections from a number of metazoan species has identified genes encoding long polyadenylated transcripts that do not contain ORFs of lengths typical for protein-encoding mRNAs. Noncoding functions of such polyadenylated transcripts have been elucidated in only a few examples. The corresponding genes neither contain hallmark sequence motifs nor appear to have been conserved across phyla. Thus, it is impossible to systematically identify new members of this class of gene by using sequence homology and traditional gene-finding algorithms that depend on protein-coding potential. Consequently, even their approximate number has not been established for any metazoan genome. We curated polyadenylated transcripts with limited protein-coding capacity from intergenic regions of the Drosophila melanogaster genome. We used RT-PCR assays, hybridization to RNA blots and whole-mount embryos, and computational analyses to characterize candidate transcripts. We verify the structures and expression of 17 distinct, likely non-protein-coding polyadenylated transcripts. We show that the expression of many of these transcripts is conserved in other Drosophila species, indicating that they have important biological functions.
authors.affiliation: Berkeley Drosophila Genome Project and Department of Genome Sciences, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 64-121, Berkeley, CA 94720, USA.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: Tupy
authors.forename: Adina M
authors.initials: AM
authors.lastname: Bailey
authors.forename: Gina
authors.initials: G
authors.lastname: Dailey
authors.forename: Martha
authors.initials: M
authors.lastname: Evans-Holm
authors.forename: Christian W
authors.initials: CW
authors.lastname: Siebel
authors.forename: Sima
authors.initials: S
authors.lastname: Misra
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
authors.forename: Gerald M
authors.initials: GM
authors.lastname: Rubin
mesh_terms: D000818:Animals; D015152:Blotting, Northern; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D004330:Drosophila / Q000145:classification / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics*; D017344:Genes, Insect / Q000235:genetics; D023281:Genomics; D017403:In Situ Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000235:genetics; D026723:Polyadenylation; D014176:Protein Biosynthesis / Q000235:genetics; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013045:Species Specificity; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger; D022661:RNA, Untranslated