Biology Reference
In-Depth Information
gene. Transcription factor-binding sites within the cis-
regulatory sequences which affect the expression of their
associated genes provide the endpoints of the regulatory
linkages. If multiple cis-regulatory modules have been
identified for a given gene, these modules can be repre-
sented by separate horizontal bars to reflect the regulatory
logic specific for each module. In the example shown in
Figure 11.2
this representation is used for the genes delta
and tbr, for example.
Regulatory interactions: The physical interaction
between transcription factors and DNA is directional in
terms of biological information flow: the gene encoding the
regulating input affects the expression of its target gene.
The linkages between nodes in the BioTapestry GRN
models therefore have a beginning and an end. This
directionality is crucial for the causality of the entire
process, which is also directional. Development never goes
backwards. In the BioTapestry model, the linkage ends with
an arrow if the transcription factor activates its target gene,
whereas a small horizontal bar indicates repression.
Levels of experimental evidence: The BioTapestry
model is based on several kinds of experimental evidence.
First and foremost, every effort is made to include all
regulatory genes specifically expressed at the relevant time
and place that might perform a role in the control system
(the total regulatory gene set is predicted from the genomic
sequence). Information regarding the temporal course of
regulatory gene expression and the exact spatial expression
pattern, which is often dynamic, is essential. The key
experimental evidence is obtained by perturbation analyses.
Trans-perturbations are performed by blocking the expres-
sion of given genes followed by determination of the effects
on all other genes in the system. This in itself is insufficient
to distinguish between direct and indirect interactions. Cis-
perturbations can accomplish this by demonstrating the
specific import of cis-regulatory target sites for factors
indicated by the trans-perturbations. Furthermore, it is to be
noted that, as the analysis becomes more complete, multiple
pieces of evidence bear on each node of the network. Details
regarding the various kinds of evidence supporting the
linkages in
Figure 11.2
can be found at (
http://sugp.caltech.
Spatial domains: The potential for all regulatory
interactions is present in the genome of every cell of the
organism. However, specific regulatory interactions are
activated regionally, in specific spatial domains of the
embryo. To represent regulatory interactions according to
the process they drive, the network model in
Figure 11.2
contains several colored rectangles labeled with the name
of the respective embryonic domain in which the specifi-
cation process occurs. Where the same regulatory gene is
utilized in different spatial domains, it is shown separately
in each network context in which it participates. This
representation strategy preserves evidence of functionality
which would be lost in a model in which each regulatory
gene and its interactions would be represented only once,
irrespective of the developmental process to which it
pertains.
Temporal dynamics: Regulatory interactions occur in
specific temporal windows. This information is not
included in the two-dimensional GRN model in
Figure 11.2
, but is available online (
http://sugp.caltech.edu/
endomes/#BioTapestryViewer
)
. In this continuously upda-
ted online version, regulatory interactions and regulatory
genes are shown in gray as long as they are not active.
A time-slider allows views of the GRN model at 3-hour
intervals covering the entire process.
Signaling interactions: Signaling interactions occur
between cells expressing a signaling ligand and cells
expressing the cognate signaling receptor. Signaling is
particularly important because it enables a specific GRN
active in a given spatial domain to alter network function in
another domain. Genes encoding signaling ligands and
receptors are controlled by the inputs into them that are
explicit in the GRNs, just as for other genes. However, the
interactions between ligand and receptor occur in intercel-
lular compartments. Reception of the signal activates an
intracellular signaling cascade off the DNA, represented by
a white circle in the BioTapestry model. Ultimately, the
signal transduction biochemistry affects the function of an
already present transcription factor (an immediate early
response factor e.g., Suppressor of Hairless for Delta/Notch
signaling or Tcf for Wnt signaling). Upon activation, the
immediate early response factor induces novel regulatory
gene expression. In the absence of the signaling interac-
tions, this factor frequently associates with a co-repressor
molecule and functions as a dominant repressor of the same
target genes.
Predictive value: The BioTapestry model is designed to
represent specific predictions of the genome-level interac-
tions that constitute a whole developmental control system.
At each individual node the requisite target site sequences
are specifically implied, and these predictions are in turn
amenable to direct experimental testing.
THE REGULATORY STATE CONCEPT
GRNs encode long chains of logic transactions. The result
of these transactions is the developmental formulation of
regulatory states. Regulatory states are defined by the
combination of specifically expressed transcription factors
and signaling molecules that discriminates these cells from
others. But the individual components of regulatory states,
that is, specific transcription factors, are rarely used in
a uniquely specific developmental context but frequently
recur in multiple regulatory states. All downstream func-
tions in development are specified and driven by the regu-
latory state expressed at each time and place in the process.
