Conservation of enhancer location in divergent insects

Abstract

Dorsoventral (DV) patterning of the Drosophila embryo is controlled by a concentration gradient of Dorsal, a sequence-specific transcription factor related to mammalian NF-B. The Dorsal gradient generates at least 3 distinct thresholds of gene activity and tissue specification by the differential regulation of target enhancers containing distinctive combinations of binding sites for Dorsal, Twist, Snail, and other DV determinants. To understand the evolution of DV patterning mechanisms, we identified and characterized Dorsal target enhancers from the mosquito Anopheles gambiae and the flour beetle Tribolium castaneum. Putative orthologous enhancers are located in similar positions relative to the target genes they control, even though they lack sequence conservation and sometimes produce divergent patterns of gene expression. The most dramatic example of this conservation is seen for the ''shadow'' enhancer regulating brinker: It is conserved within the intron of the neighboring Atg5 locus of both flies and mosquitoes. These results suggest that, like exons, an enhancer position might be subject to constraint. Thus, novel patterns of gene expression might arise from the modification of conserved enhancers rather than the invention of new ones. We propose that this enhancer constancy might be a general property of regulatory evolution, and should facilitate enhancer discovery in nonmodel organisms.

Multiple layers of complexity in cis‐regulatory regions of developmental genes

“…Developmental genes bear substantial regulatory information, and, so far, we ignore whether the spatial distribution of regulatory elements follows a particular set of rules. In this regard, recent reports show that some transcriptional enhancers maintain their positions in cis-regulatory regions of distant species (Hare et al, 2008;Cande et al, 2009;Frankel, Wang, and Stern, unpublished). These data suggest the existence of constraints in the architecture of cis-regulatory regions, although not much more is known about the large scale organization of cis-regulatory regions.…”

Comparative genomics of gene regulation—conservation and divergence of cis-regulatory information

“…Enhancers have been found thousands of base pairs upstream or downstream of the regulated gene, in the gene's or in neighboring genes' introns, and even work across intervening genes (e.g. [2,3]). While this indicates that the relative location of enhancers can be highly variable, some enhancers' positions are constrained, such as a distal enhancer of brinker in Drosophila and mosquitoes [3], or the Hox gene cluster (see discussion in [3]).…”

The evolution of dorsal–ventral patterning mechanisms in insects

“…One such discovery was that, despite having no clear homology at the nucleic acid level, CRMs driving DV patterning gene expression are very often located in comparable genomic locations over quite large evolutionary distances (Cande et al 2009), indicating that CRMs may behave more similarly to exons in the course of evolution than would have been expected. Another discovery was the concept of the ''shadow'' enhancers, which are elements that often reside quite distant from their targets, but drive similar patterns of expression to already described CRMs.…”

“…The presence of such redundant elements may provide raw material for evolutionary change without disrupting a running system. Interestingly, the ''shadow'' enhancer of brk, which is located in an intron of a flanking gene in Drosophila, is conserved in the mosquito Anopheles (Cande et al 2009), indicating that the position of this enhancer has been conserved through 100 million years of evolution. Thus, it appears that shadow enhancers can be maintained selectively over evolutionary time, and it will be interesting to see whether these redundant enhancers are subject to similar processes that affect duplicated protein-coding genes (e.g., neofunctionalization, subfunctionalization, or nonfunctionalization) (Force et al 1999).…”