Fig. 1.
Identification of Dl targets using a whole-genome tiling array. (a) (Left) The expression patterns of six previously characterized Dl target genes: dpp (dorsal ectoderm); ind, vnd, rho, sog (neuroectoderm); and sna (mesoderm). Embryos are all oriented with anterior to the left, and dorsal is up. (Right) Shown, for each of the six genes, are the RNA signal graphs from three mutant backgrounds as viewed in the Affymetrix Integrated Genome Browser (Affymetrix). The top (blue) graph represents total cellular transcripts from pipe−/pipe− mutants; the middle (orange) graph represents transcripts from Tollrm9/Tollrm10 mutant embryos; and the bottom (pink) graph represents transcripts in Toll10B mutant embryos. (b) Classical genetic studies previously characterized ≈30 Dl target genes (small circle, pale green). Microarray analysis identified between 20 and 40 additional targets (intermediate circle, light green; ref. 7). In the present study, the unbiased survey of the entire genome using tiling arrays identified as many as ≈30 additional protein-coding genes (large circle, dark green). (c) In addition to the protein-coding Dl target genes, 23 uncharacterized transfrags were identified that represent previously unidentified 3′ exons (13%; 3 of 23) or 5′ exons (48%; 11 of 23) of known protein-coding genes. The remaining nine transfrags correspond to putative new genes (39%; 9 of 23).