  Background: Duplication of genes is important for evolution of molecular
networks. Many authors have therefore considered gene duplication as a driving
force in shaping the topology of molecular networks. In particular it has been
noted that growth via duplication would act as an implicit way of preferential
attachment, and thereby provide the observed broad degree distributions of
molecular networks.
  Results: We extend current models of gene duplication and rewiring by
including directions and the fact that molecular networks are not a result of
unidirectional growth. We introduce upstream sites and downstream shapes to
quantify potential links during duplication and rewiring. We find that this in
itself generates the observed scaling of transcription factors for genome sites
in procaryotes. The dynamical model can generate a scale-free degree
distribution, p(k)&prop; 1/k^&gamma;, with exponent &gamma;=1 in the
non-growing case, and with &gamma;>1 when the network is growing.
  Conclusions: We find that duplication of genes followed by substantial
recombination of upstream regions could generate main features of genetic
regulatory networks. Our steady state degree distribution is however to broad
to be consistent with data, thereby suggesting that selective pruning acts as a
main additional constraint on duplicated genes. Our analysis shows that gene
duplication can only be a main cause for the observed broad degree
distributions, if there is also substantial recombinations between upstream
regions of genes.
