The fushi tarazu pair-rule gene is required for the formation of alter
nating parasegmental boundaries in the Drosophila embryo, fushi tarazu
encodes a homeodomain protein necessary for transcription of the engr
ailed gene in even-numbered parasegments, Here we report that, within
an engrailed enhancer, adjacent and conserved binding sites for the Fu
shi tarazu protein and a cofactor are each necessary, and together suf
ficient, for transcriptional activation, Footprinting shows that the c
ofactor site can be bound specifically by Ftz-F1, a member of the nucl
ear receptor superfamily, Ftz-F1 and the Fushi tarazu homeodomain bind
the sites with 4- to 8-fold cooperativity, suggesting that direct con
tact between the two proteins may contribute to target recognition, Ev
en parasegmental reporter expression is dependent on Fushi tarazu and
maternal Ftz-F1, suggesting that these two proteins are indeed the fac
tors that act upon the two sites in embryos, The two adjacent binding
sites are also required for continued activity of the engrailed enhanc
er after Fushi tarazu protein is no longer detectable, including the p
eriod when engrailed, and the enhancer, become dependent upon wingless
. We also report the existence of a separate negative regulatory eleme
nt that apparently responds to odd-skipped.