If this theory is correct, we would expect the evolution of the gene
regulatory network to be heterogeneous. The “kernels” module
should evolve more slowly than other parts of the gene regulatory
network, since the phylum- and superphylum-level body plan
characteristics have not changed substantially since the early
Cambrian. The gene regulatory networks are primarily composed of
two elements: transcription factors and cis-regulatory modules.
Transcription factors are proteins that can either activate or repress
transcription by binding to cis-regulatory elements. Transcription
factor binding sites are often organized into clusters named cisregulatory
modules, which typically span a few hundred nucleotides
and can contain dozens of binding sites for several transcription
factors (Chen and Rajewsky, 2007). A full understanding of the
evolution of the gene regulatory network would consider both
transcription factors and cis-regulatory modules. cis-Regulatory
modules are poorly conserved during evolution, and even in closely
related species may differ drastically (Wray, 2007; Chen and
Rajewsky, 2007). Because experimental identification of cis-regulatory
elements is still not well developed, and because computational
prediction of cis-regulatory elements is still difficult (Elnitski et al.,
2006), we considered only evolution of the transcription factors.
Transcription factors are more conserved and evolve more slowly
than cis-regulatory elements. On the timescale of hundreds of millions
of years that we consider here, it is important to consider the
evolution of transcription factor networks. For example, acquisition of
an extra repressive regulatory domain in the insect protein Ubx