Sea urchin embryos are though to possess a body plan characteristic of earl
y deuterostomes. Sea urchins contain homologs of Otx, Lim, T-brain and Hox
gene cluster, which are involved in head and segment formation in vertebrat
e development, although the sea urchin has not evolved a head or segments.
We described here that sea urchin Otx is involved in various aspects of ear
ly development and that the Hox genes do not obey spatial colinearity in se
a urchin embryo. The Otx and Hox genes seems to be used subsequently for he
ad formation and determining the anteroposterior axis respectively during c
hordate evolution. We propose that the Precambrian was a period where these
regulatory genes were utilized in many different combinations during anima
l development, leading to the evolution of a wide range of body plans, many
of which were successful. We also discuss the role of chromatin boundaries
and the mechanism of cell specification along animal vegetal axis, especia
lly differentiation of the large micromere progeny, which are the prospecti
ve primary mesenchyme cells and play a role as an organizer in sea urchin e
mbryos.