Previous studies have identified a minimal 434 bp enhancer from the pr
omoter region of the Ciona Brachyury gene (Ci-Bra a), which is suffici
ent to direct a notochord-specific pattern of gene expression. Here we
present evidence that a Ciona homolog of snail (Ci-sna) encodes a rep
ressor of the Ci-Bra enhancer in the tail muscles. DNA-binding assays
identified four Ci-Sna-binding sites in the Ci-Bra enhancer, and mutat
ions in these sites cause otherwise normal Ci-Bra/lacZ transgenes to b
e misexpressed in ectopic tissues, particularly the tail muscles. Sele
ctive misexpression of Ci-sna using a heterologous promoter results in
the repression of Ci-Bra/lacZ transgenes in the notochord. Moreover,
the conversion of the Ci-Sna repressor into an activator results in th
e ectopic induction of Ci-Bra/lacZ transgenes in the muscles, and also
causes an intermixing of notochord and muscle cells during tail morph
ogenesis. These results suggest that Ci-Sna functions as a boundary re
pressor, which subdivides the mesoderm into separate notochord and tai
l muscle lineages.