Evolving enhancer-promoter interactions within the tinman complex of the flour beetle,Tribolium castaneum

Abstract

Modifications of cis-regulatory DNAs, particularly enhancers, underlie changes in gene expression during animal evolution. Here, we present evidence for a distinct mechanism of regulatory evolution, whereby a novel pattern of gene expression arises from altered gene targeting of a conserved enhancer. The tinman gene complex (Tin-C) controls the patterning of dorsal mesodermal tissues, including the dorsal vessel or heart in Drosophila. Despite broad conservation of Tin-C gene expression patterns in the flour beetle (Tribolium castaneum), the honeybee (Apis mellifera) and the fruit fly (Drosophila melanogaster), the expression of a key pericardial determinant, ladybird, is absent from the dorsal mesoderm of Tribolium embryos. Evidence is presented that this loss in expression is replaced by expression of C15, the neighboring gene in the complex. This switch in expression from ladybird to C15 appears to arise from an inversion within the tinman complex, which redirects a conserved ladybird 3Ј enhancer to regulate C15. In Drosophila, this enhancer fails to activate C15 expression owing to the activity of an insulator at the intervening ladybird early promoter. By contrast, a chromosomal inversion allows the cardiac enhancer to bypass the ladybird insulator in Tribolium. Given the high frequency of genome rearrangements in insects, it is possible that such enhancer switching might be widely used in the diversification of the arthropods.

Novel functions for Dorsocross in epithelial morphogenesis in the beetle Tribolium castaneum

“…Additionally, Tc-Doc expression appears in a metameric fashion within the dorsal mesoderm (Fig. 2E,F, red arrows), where the conserved mesodermal marker Tc-Mef2 is also expressed (Cande et al, 2009) and similar to Dm-Doc (Reim et al, 2003). However, we could not detect Tc-Doc in the cardioblast mesodermal derivatives at later stages (Fig.…”

Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression

“…3B). This would suggest that the native context of CRMs within a locus can limit interactions between elements, and may go towards explaining why enhancers in diverged species/animals tend to be found in the same general location (Cande et al, 2009;Hare et al, 2008). Similarly, the dampening of all snail expression patterns we observe in the 'D to P' construct may be due to the repressive activity of the distal CRM being moved near the promoter.…”

Dissecting the regulatory switches of development: lessons from enhancer evolution in Drosophila

“…These crucial developmental genes cannot, therefore, be expressed ubiquitously. A number of emerging studies indicate that these specific promoterenhancer interactions are subject to subtle molecular control mechanisms, including the activity of a novel class of regulatory module -the promoter tethering element (Akbari et al, 2008;Akbari et al, 2007;Calhoun et al, 2002;Cande et al, 2009;Fujioka et al, 2009;Kwon et al, 2009).…”

“…However, what does appear to be under (1) evolutionary constraint is the position of these enhancers relative to their target gene. As a result, as these enhancers are modified over evolutionary time, they become capable of directing divergent patterns of gene expression (Cande et al, 2009).…”