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In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression Biological development depends on the coordinated expression of genes in time and space. Developmental genes have extensive cis-regulatory regions which control their expression. These regions are organized in a modular manner, with different modules controlling expression at different times and locations. Both how modularity evolved and what function it serves are open questions. We present a computational model for the cis-regulation of the hunchback (hb) gene in the fruit fly (Drosophila). We simulate evolution (using an evolutionary computation approach from computer science) to find the optimal cis-regulatory arrangements for fitting experimental hb expression patterns. We find that the cis-regulatory region tends to readily evolve modularity. These cis-regulatory modules (CRMs) do not tend to control single spatial domains, but show a multi-CRM/multi-domain correspondence. We find that the CRM-domain correspondence seen in Drosophila evolves with a high probability in our model, supporting the biological relevance of the approach. The partial redundancy resulting from multi-CRM control may confer some biological robustness against corruption of regulatory sequences. The technique developed on hb could readily be applied to other multi-CRM developmental genes.,Peer reviewed,Published. 2014-04 doi: 10.1142/S0219720014410091 accessnum: NIHMS583031 pmc: PMC4068237 English Holloway, David Zagrijchuk, Elizaveta A. Sabirov, Marat A. Spirov, Alexander V. Imperial College Press Text © 2014 Imperial College Press