DETECTING CONSERVED REGULATORY ELEMENTS WITH THE MODEL GENOME OF THE JAPANESE PUFFER FISH, FUGU RUBRIPES

Comparative vertebrate genome sequencing offers a powerful method for detecting conserved regulatory sequences. We propose that the compact genome of the teleost Fugu rubripes is well suited for this purpose. T he evolutionary distance of teleosts from other vertebrates offers the maximum stringency for such evolutionary comparisons, To illustrate t he comparative genome approach for F. rubripes, we use sequence compar isons between mouse and Fugu Hoxb-4 noncoding regions to identify cons erved sequence blocks, We have used two approaches to test the functio n of these conserved blocks, In the first, homologous sequences were d eleted from a mouse enhancer, resulting in a tissue-specific loss of a ctivity when assayed in transgenic mice, In the second approach, Fugu DNA sequences showing homology to mouse sequences were tested for enha ncer activity in transgenic mice. This strategy identified a neural el ement that mediates a subset of Hoxb-4 expression that is conserved be tween mammals and teleosts. The comparison of noncoding vertebrate seq uences with those of Fugu, coupled to a transgenic bioassay, represent s a general approach suitable for many genome projects.