Evolutionary and functional analysis of the tailless enhancer in Musca domestica and Drosophila melanogaster

Abstract

To further understand the evolutionary dynamics of the regulatory interactions underlying development, we expand on our previous analysis of hunchback and compare the structure and function of the tailless enhancer between Musca domestica and Drosophila melanogaster. Our analysis shows that although the expression patterns and functional protein domains of tll are conserved between Musca and Drosophila, the enhancer sequences are unalignable. Upon closer investigation, we find that these highly diverged enhancer sequences encode the same regulatory information necessary for Bicoid, Dorsal, and the terminal system to drive tll expression. The binding sites for these transcription factors differ in the sequence, number, spacing, and position between the Drosophila and Musca tll enhancers, and we were unable to establish homology between binding sites from each species. This implies that the Musca and Drosophila Bcd-binding sites have evolved de novo in the 100 million years since these species diverged. However, in transgenic Drosophila embryos the Musca tll enhancer is able to drive the same expression pattern as endogenous Drosophila tll. Therefore, during the rapid evolution of enhancer sequences individual binding sites are continually lost and gained, but the transcriptional output is maintained by compensatory mutations in cis and in trans.

Cis-regulation of the amphioxus engrailed gene: Insights into evolution of a muscle-specific enhancer

“…Moreover, even when the enhancer sequences are conserved, the enhancers themselves may occupy different positions in relation to the gene that is regulated and, therefore, may not be detected in alignments of large DNA segments. For example, comparisons of the housefly and fruitfly, showed that even though the domain of tll expression is conserved, the enhancer sequences that direct expression cannot be aligned, and neither the sequence of the enhancer nor the sequence, number, spacing and position of the binding sites that direct expression are conserved (Wratten et al, 2006). Therefore, it is perhaps not surprising that there are no alignable regions of upstream engrailed DNA between amphioxus and C. intestinalis even though both genes are expressed in the CNS.…”

Genome clashes in hybrids: insights from gene expression

“…Early studies included those on Caenorhabditis and vertebrates, in which it was noticed that interspecific differences in expression profiles can be the result of changes in the regulatory sequences upstream of particular genes critical during development (Belting et al, 1998;Wang and Chamberlin, 2002). These changes in gene expression can be due to de novo evolution of regulatory sequences (Gonzalez et al, 1995;Papaceit et al, 2004;Wratten et al, 2006), although a large number of studies indicate that their evolution often involves the rearrangement and modification of sequences with known regulatory roles (Gompel et al, 2005;Prud'-homme et al, 2006). In several cases, mutations in cisregulatory sequences imply gains or losses of binding sites for key selector genes in a lineage-specific manner leading to complex changes in the patterns of gene expression.…”

“…Another example comes from the study of the Bicoid (Bcd)-binding sites in the upstream of the genes hunchback (hb) and tailless (tll) of D. melanogaster and the house fly Musca domestica. This study combined transgenics with in vitro binding assays to provide one of the first comparative measures of the extent of regulatory incompatibility between species (Shaw et al, 2002;Wratten et al, 2006). There is not only evidence for coevolution between the trans-and cis-regulatory elements, but also evidence that the incompatibility does not result in a reduced binding, but rather higher affinity.…”

Emerging principles of regulatory evolution

“…And finally, there have been few detailed functional studies of CRE evolution. Most studies have focused on the functional conservation of CREs (18)(19)(20). Until very recently, there have been very few direct empirical examples linking CRE evolution to morphological evolution (21,22).…”