Expression profile of the first 24 hrs of Drosophila embryonic development using tiling arrays

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. To begin to address this question, we have generated a series of transcription maps at an interrogation resolution of 35 base pairs (bp) across the Drosophila genome for the first 24 hrs of development in 2 hour increments, similar to maps we have created for regions of the human genome. Using a single tiling array, 3,075,693 probe pairs of twenty-five nucleotides (nts) in length were used to interrogate 105,897,358 non-repeat bp of the fly genome. Maps of the sites of transcription were made using total RNA greater than 200 nts. 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. 15.6 % of intergenic transcribed regions function as missed or alternative transcription start sites utilized 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. Keywords: time course, Drosphila embryonic development, tiling array, expression profile Total RNA was extracted from dechorionated whole embryos collected in 2hr intervals (0-2 hr, 2-4hr..etc)for 12 time points (first 24hr of development). RNA was then converted to cDNA using standard protocols. 3 replicate chips were used for each sample (time point).