Biological function of unannotated transcription during the early development of Drosophila melanogaster.
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.
Manak
J Robert
JR
Affymetrix, Inc., Santa Clara, California, 95051, USA. John_Manak@affymetrix.com
Dike
Sujit
S
Sementchenko
Victor
V
Kapranov
Philipp
P
Biemar
Frederic
F
Long
Jeff
J
Cheng
Jill
J
Bell
Ian
I
Ghosh
Srinka
S
Piccolboni
Antonio
A
Gingeras
Thomas R
TR
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
D021901:DNA, Intergenic; D029721:Drosophila Proteins