We describe a transcriptional analysis platform consisting of a universal micro-array system (UMAS) combined with an enzymatic manipulation step that is capable of generating expression profiles from any organism without requiring a priori species-specific knowledge of transcript sequences. The transcriptome is converted to cDNA and processed with restriction endonucleases to generate low-complexity pools (approximately 80-120) of equal length DNA fragments. The resulting material is amplified and detected with the UMAS system, comprising all possible 4,096 (4(6)) DNA hexamers. Ligation to the arrays yields thousands of 14-mer sequence tags. The compendium of signals from all pools in the array-of-universal arrays comprises a full-transcriptome expression profile. The technology was validated by analysis of the galactose response of Saccharomyces cerevisiae, and the resulting profiles showed excellent agreement with the literature and real-time PCR assays. The technology was also used to demonstrate expression profiling from a hybrid organism in a proof-of-concept experiment where a T-cell receptor gene was expressed in yeast.

Proteins containing an expanded polyglutamine tract are neurotoxins. The expanded polyglutamine proteins influence a variety of cellular functions. In Drosophila the GMR-Gal4/UAS expression system has been widely used in an eye-based model to study human neurodegenerative diseases. This system has facilitated the isolation and characterization of abundant Drosophila genes that interact with the expanded polyglutamine proteins. We used the GMR-Gal4/UAS system to express three proteins containing an expanded polyglutamine tract, or an expanded polyglutamine tract alone. Doubling the dose of these proteins resulted in pupal lethality, indicating that these toxic proteins induced a sensitized condition that is prone to synthetic lethality. By using the GMR-Gal4/UAS system, we showed that a Drosophila gene interacts with three expanded polyglutamine proteins to induce a synthetic lethal phenotype. We further demonstrated that the synthetic lethality was mediated through the toxic expanded polyglutamine tract. Our study raises a possibility that conventional genetic screens may not recover synthetic lethal alleles, which are presumably stronger interacting alleles than the currently known modifiers of an expanded polyglutamine tract, due to synthetic lethality.

We isolated a set of seven deletions in the 67B region by activating a nearby P-element insertion. The structures of the deletions were characterized by cloning and sequencing. The results showed that the P-induced deletions occurred nonrandomly in the genomic sites. One breakpoint of the deletions was located precisely at the end of the starting element, i.e., at the end of the inverted terminal repeats. The other breakpoint was nearby the retained starting element and coincided with preferential P-element insertion sites that harbor transcription initiation activities. It is known that P elements induce male recombination near the starting elements, giving rise to deletions with one breakpoint precisely located at an inverted terminal repeat of the retained starting element. Database analyses further revealed that deletions generated in P-induced male recombination also contained the other breakpoint in genomic regions that coincided with preferential P-insertion sites. The results suggest that nonrandom distribution of the deletion breakpoints is characteristic of the mechanism by which P elements induce deletions near the starting elements.