title: Biological function of unannotated transcription during the early development of Drosophila melanogaster.
abstract: Many animal and plant genomes are transcribed much more extensively than current annotations predict. However, the biological function of these unannotated transcribed regions is largely unknown. Approximately 7% and 23% of the detected transcribed nucleotides during D. melanogaster embryogenesis map to unannotated intergenic and intronic regions, respectively. Based on computational analysis of coordinated transcription, we conservatively estimate that 29% of all unannotated transcribed sequences function as missed or alternative exons of well-characterized protein-coding genes. We estimate that 15.6% of intergenic transcribed regions function as missed or alternative transcription start sites (TSS) used by 11.4% of the expressed protein-coding genes. Identification of P element mutations within or near newly identified 5' exons provides a strategy for mapping previously uncharacterized mutations to their respective genes. Collectively, these data indicate that at least 85% of the fly genome is transcribed and processed into mature transcripts representing at least 30% of the fly genome.
authors.affiliation: Affymetrix, Inc., Santa Clara, California, 95051, USA. John_Manak@affymetrix.com
authors.forename: J Robert
authors.initials: JR
authors.lastname: Manak
authors.forename: Sujit
authors.initials: S
authors.lastname: Dike
authors.forename: Victor
authors.initials: V
authors.lastname: Sementchenko
authors.forename: Philipp
authors.initials: P
authors.lastname: Kapranov
authors.forename: Frederic
authors.initials: F
authors.lastname: Biemar
authors.forename: Jeff
authors.initials: J
authors.lastname: Long
authors.forename: Jill
authors.initials: J
authors.lastname: Cheng
authors.forename: Ian
authors.initials: I
authors.lastname: Bell
authors.forename: Srinka
authors.initials: S
authors.lastname: Ghosh
authors.forename: Antonio
authors.initials: A
authors.lastname: Piccolboni
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D021901:DNA, Intergenic; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000196:embryology* / Q000235:genetics*; D004625:Embryo, Nonmammalian; D005091:Exons; D018507:Gene Expression Regulation, Developmental; D049750:Genome, Insect; D008969:Molecular Sequence Data; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D021901:DNA, Intergenic; D029721:Drosophila Proteins