Transcriptional Network Logic: The Systems Biology of Development - Systems Biology Concepts and Insights - page 211

the interior of the embryo, their position and further
differentiation depend on signals emanating from their
newly neighboring cells [71] . One of these signals
( Figure 11.4 A, 'Signal 3') is VEGF and the gene encoding
its receptor (VEGFR) is transcribed under control of the
skeletogenic GRN ( Figure 11.4 C).

fates. In the sea urchin embryo, the endoderm and meso-
derm share a common progenitor cell lineage. Curiously,
the mesodermal GRN and the endodermal GRN run
simultaneously in these cells with no regulatory interac-
tions between them ( Figure 11.5 A, red and blue networks)
[53] . The activation of the GRNs occurs by using separate
inputs, Delta/Notch signaling vs. Wnt signaling. Definitive
separation of fates makes use of a canonical radial cleavage
which separates an inner ring of cells destined to become
mesoderm and an outer ring destined to become endoderm.
The relation between regulatory state and these rings of
cells is shown diagrammatically in Figure 11.5 B, where
endoderm fate is represented in red and mesoderm in green.
Initially, both GRNs continue to operate in the inner ring of
cells, but the circuitry shown in Figure 11.5 C results in the
extinction of the endodermal network in the inner ring of
cells. Delta/Notch signaling, which is accessible only to the
inner ring, because these cells are adjacent to the source of
the Delta ligand (the skeletogenic cells, yellow in
Figure 11.5 B), is used to shut down endodermal regulatory
genes [15,68] . Note that even before the definitive fate
separation the progenitor cells are not 'bi-stable': which of
their descendants are going to be mesodermal and which
endodermal is hardwired.
The general import of these examples is that they
illustrate in (minimum) detail exactly how GRN architec-
ture results in direct and specific control of spatial regula-
tory state. In turn, viewing network circuitry in its
developmental context illuminates the stepwise path of the
developmental process.

Example 4: Parallel Mechanisms in Cell Fate
Initiation

In the GRNs for the sea urchin endomesoderm we see
repeatedly that the initial establishment of a spatial regu-
latory domain usually depends on a single regulatory input.
Thus, mesoderm specification depends on the Delta/Notch
signal from adjacent skeletogenic cells; endoderm specifi-
cation requires Wnt signaling; and in the skeletogenic cells
specification depends on transcription of pmar1. In all three
domains, what begins with a unitary spatial input ends with
the activation of a complex network of regulatory interac-
tions. The progressive activation of a network of transcrip-
tional interactions requires multiple regulatory steps and in
the sea urchin embryo takes many hours to attain its
terminal state. In all three cases the upstream input mediates
a switch logic, such that the system is either repressed or
activated in different locations. This 'bottleneck' aspect of
the specification mechanism contributes in both evolution
and development to a Boolean process of regional fate
assignment.

Example 5: Mechanism of Irreversibility in the
Developmental Process
Downstream of the early spatial activation system there
predictably appears a network subcircuit which ensures the
continued expression of regulatory genes even when the
early inputs are no longer available. In the skeletogenic
GRN, pmar1 is expressed only transiently [64] , but
immediately downstream of the double-negative gate target
genes there exists a triple positive feedback circuit [14] .
These three genes maintain each other's expression, and
once the system is activated it no longer requires the initial
skeletogenic inputs. Similar positive feedback circuitry can
be found in the mesoderm specification GRN ( Figure 11.2 ,
'aboral NSM') downstream of the initial Delta/Notch
signaling input [72] . Here again, the circuitry renders the
subsequent regulatory state independent of continued
signaling input. These positive feedbacks ensure that the
regulatory state instructed by the signal or other transient
initial input is maintained and cannot revert to the previous
regulatory state.

CONCLUSION: THE EXPLANATION
OF DEVELOPMENT
What would be the anatomy of an explanation of a devel-
opmental process of embryogenesis or body part forma-
tion? First, it must encompass all the parts of the apparatus
that play a causal role, so that it is a system-wide and not an
island-like explanation. Second, it should be predictive of
the spatial innovations entailed in the process, so that the
mechanism included in the explanation and the status at
each given step should suffice to predict the next step.
Third, it should be causally progressive, so that it captures
the dynamics of the process. Fourth, it should be commu-
tative, so that the mechanistic argument leads smoothly,
without gaps, going either upstream from the observed
developmental process back to the genome, or downstream
from the genome to the observed developmental process.
Everything that happens in development depends
causally on spatially defined regulatory states, and the
process that embryologists used to call specification is
neither more nor less than the installation of these regula-
tory states. Thus if we can explain the process of

Example 6: GRN-Mediated Cell Fate Decision
It is often found that in embryonic development a discrete
progenitor cell population gives rise to multiple diverse cell