UNDERSTANDING THE MECHANISMS OF TRANSCRIPTIONAL ROBUSTNESS DURING EMBRYONIC DEVELOPMENT.

Embryos develop into stereotypically patterned organisms that are largely robust to differences in segregating mutations and environmental conditions. Such robustness is in part conferred through elements that perform similar, and thus partially redundant, tasks. Partially redundant enhancers, for example, confer precision and robustness to gene expression during development, as shown at individual, well-studied loci. However, the extent to which enhancer redundancy exists and can thereby have a major impact on developmental robustness remains unknown. Here, we systematically address this question, identifying over 2,000 predicted pairs of partially redundant enhancer elements (PREEs) during Drosophila mesoderm development. The activity of 28 specific elements, distributed throughout 7 loci, was compared in transgenic embryos, while natural sequence variation – i.e, structural variation – among ‘individuals’ was used to assess their potential redundancy. Our results reveal three clear properties of enhancer redundancy within developmental systems. First, enhancer redundancy is much more pervasive than previously anticipated, with 70% of loci examined having two or more PREEs. Second, over 50% of tested loci do not follow the simple situation of having only two redundant elements as generally assumed – often there are three (rols), four (CadN and ade5) or even five (Traf1) enhancers with overlapping spatio-temporal activity, where at least one of which can be deleted without obvious phenotypic effects. Third, this level of potential robustness in transcriptional regulation is not reserved for the key developmental regulators, or selector genes, but rather many genes regardless of their function have extensive levels of cis-regulatory redundancy.