Identification of genome-wide homeotic target genes in Drosophila melanogaster. J.C. Kim¹, M. Ghanim¹, R.S. Mann², K.P. White¹. 1) Genetics, Yale University, New Haven, CT; 2) Biochemistry and Molecular Biophysics, Columbia University, New York, NY.

   The homeotic genes encode transcription factors that control segmental identity along the anterior-posterior axis. Despite this important biological function, very little is known about downstream targets, particularly on a genome-wide level. To address questions of homeotic protein target gene number, regulatory function, and specificity, an approach combining compound homeotic mutants and microarray technology was performed. Six mutant strains were chosen for genomic microarray analysis: (1) Ubx- (2) Scr-, Antp-, Ubx-, abd-A-, Abd-B- or ground state (3) Scr-, Antp-, abd-A-, Abd-B- or Ubx+ (4) Antp- (5) Scr-, Ubx-, abd-A-, Abd-B- or Antp+ and (6) wild type. Homozygous mutant embryos were collected at stage 7 to identify the most likely direct targets and hybridized against a common reference sample to Drosophila DNA microarrays, thus allowing multiple pair-wise comparisons. Because of posterior dominance we expected to get an underestimate of the true number of downstream targets using single mutants, that is, wt vs Ubx- and wt vs Antp-. Nonetheless we identified over 900 novel targets and found that most targets are repressed. Still, more powerful comparisons are possible. The genotypes above labeled 2, 3, and 5 are especially useful because they allow us to compare the transcriptional response in the absence of all homeotic gene function to that in the presence of a single homeotic gene. Using such comparisons, we have found that UBX and ANTP share roughly 50% of the same downstream targets. In addition, UBX and ANTP each have unique targets that may account for their segment-specific morphological effects; for example some ANTP specific targets appear to be involved in imaginal disc and wing development. Follow-up studies of such genes should shed new light on the mechanisms by which the homeotic genes direct segmental identity.