Echinoderms are the sister group of the chordates and hemichordates wi
thin the deuterostomes. They lack a notochord or any structures obviou
sly homologous with it. To gain insight into developmental mechanisms
important in the origin and early evolution of chordates, we investiga
ted sea urchin homologues of chordate genes that are implicated in not
ochord formation, viz. Brachyury and HNF-3 beta. Here we report the pa
ttern of expression of a sea urchin orthologue of forkhead, Hphnf3 whi
ch is present as a single copy per haploid genome. An Hphnf3 transcrip
t of 3.0 kb was first detected at the swimming blastula stage, accumul
ated maximally at the gastrula and prism-embryo stages, and decreased
at the pluteus-larva stage. In situ hybridization signals were found i
n cells of the vegetal plate of the swimming blastula. During gastrula
tion, intense staining was evident in the cells surrounding the blasto
pore, whereas weak staining was detected in the invaginating archenter
on. At the prism-embryo stage, the entire archenteron stained intensel
y; then, at pluteus stage, the larva staining decreased in intensity.
The forkhead and Brachyury genes begin to be expressed almost simultan
eously in sea urchin embryos, in the vegetal plate at the late blastul
a stage. After the onset of gastrulation, however, Hphnf3 is expressed
in the posterior part of the archenteron, whereas the Brachyury ortho
logue, HpTa, is expressed in the secondary mesenchyme founder cells, w
hich occupy the anterior tip of archenteron. Hphnf3 may contribute to
specification of embryonic cells as archenteron, and the role of HpTa
may be directed towards specification of mesodermal founder cells. Exc
ept for the basal character of expression in endoderm and endomesoderm
, these transcription factors are clearly utilized differently in chor
dates.