Control of Distal-less expression in the Drosophila appendages by functional 3' enhancers

The expression of the Hox gene Distal-less (Dll) directs the development of appendages in a wide variety of animals. In Drosophila, its expression is subjected to a complex developmental control. In the present work we have studied a 17 kb genomic region in the Dll locus which lies downstream of the coding sequence and found control elements of primary functional importance for the expression of Dll in the leg and in other tissues. Of particular interest is a control element, which we have called LP, which drives expression of Dll in the leg primordium from early embryonic development, and whose deletion causes severe truncation and malformation of the adult leg. This is the first Dll enhancer for which, in addition to the ability to drive expression of a reporter, a role can be demonstrated in the expression of the endogenous Dll gene and in the development of the leg. In addition, our results suggest that some enhancers, contrary to the widely accepted notion, may require a specific 5′ or 3′ position with respect to the transcribed region.     

Composite cis-acting epigenetic switches in eukaryotes: lessons from Drosophila Fab-7 for the Igf2-H19 imprinted domain

One of the central problems of eukaryotic gene regulation is to understand the mechanism(s) by which the activity of enhancer elements is circumscribed such that they only act upon their cognate promoter sequences. Studies on the bithorax gene complex (BX-C) in Drosophila have highlighted the potential problem of enhancer promiscuity and detailed molecular and genetic analyses are now providing insight into how this gene complex resolves the problem through the activity of boundary/silencer elements that can block the communication between enhancers and promoters. Analysis of the mouse Igf2–H19 imprinted locus also suggests a role for boundary/silencer elements, but in this case these elements are invoked to account for the preferential expression of Igf2 and H19 from the paternally and maternally inherited chromosomes respectively despite the presence of functional downstream enhancers. We discuss recent work that has illuminated both of these systems and consider what parallels exist between them.     

Conserved boundary elements from the Hox complex of mosquito,Anopheles gambiae

The conservation of hox genes as well as their genomic organization across the phyla suggests that this system of anterior–posterior axis formation arose early during evolution and has come under strong selection pressure. Studies in the split Hox cluster of Drosophila have shown that proper expression of hox genes is dependent on chromatin domain boundaries that prevent inappropriate interactions among different types of cis-regulatory elements. To investigate whether boundary function and their role in regulation of hox genes is conserved in insects with intact Hox clusters, we used an algorithm to locate potential boundary elements in the Hox complex of mosquito, Anopheles gambiae. Several potential boundary elements were identified that could be tested for their functional conservation. Comparative analysis revealed that like Drosophila, the bithorax region in A. gambiae contains an extensive array of boundaries and enhancers organized into domains. We analysed a subset of candidate boundary elements and show that they function as enhancer blockers in Drosophila. The functional conservation of boundary elements from mosquito in fly suggests that regulation of hox genes involving chromatin domain boundaries is an evolutionary conserved mechanism and points to an important role of such elements in key developmentally regulated loci.     

Midline enhancer activity of the short gastrulation shadow enhancer is characterized by three unusual features for cis-regulatory DNA

The shadow enhancer of the short gastrulation (sog) gene directs its sequential expression in the neurogenic ectoderm and the ventral midline of the developing Drosophila embryo. Here, we characterize three unusual features of the shadow enhancer midline activity. First, the minimal regions for the two different enhancer activities exhibit high overlap within the shadow enhancer, meaning that one developmental enhancer possesses dual enhancer activities. Second, the midline enhancer activity relies on five Single-minded (Sim)-binding sites, two of which have not been found in any Sim target enhancers. Finally, two linked Dorsal (Dl)- and Zelda (Zld)-binding sites, critical for the neurogenic ectoderm enhancer activity, are also required for the midline enhancer activity. These results suggest that early activation by Dl and Zld may facilitate late activation via the noncanonical sites occupied by Sim. We discuss a model for Zld as a pioneer factor and speculate its role in midline enhancer activity. [BMB Reports 2015; 48(10): 589-594]     

Organization of developmental enhancers in the Drosophila embryo

Most cell-specific enhancers are thought to lack an inherent organization, with critical binding sites distributed in a more or less random fashion. However, there are examples of fixed arrangements of binding sites, such as helical phasing, that promote the formation of higher-order protein complexes on the enhancer DNA template. Here, we investigate the regulatory ‘grammar’ of nearly 100 characterized enhancers for developmental control genes active in the early Drosophila embryo. The conservation of grammar is examined in seven divergent Drosophila genomes. Linked binding sites are observed for particular combinations of binding motifs, including Bicoid–Bicoid, Hunchback–Hunchback, Bicoid–Dorsal, Bicoid–Caudal and Dorsal–Twist. Direct evidence is presented for the importance of Bicoid–Dorsal linkage in the integration of the anterior–posterior and dorsal–ventral patterning systems. Hunchback–Hunchback interactions help explain unresolved aspects of segmentation, including the differential regulation of the eve stripe 3 + 7 and stripe 4 + 6 enhancers. We also present evidence that there is an under-representation of nucleosome positioning sequences in many enhancers, raising the possibility for a subtle higher-order structure extending across certain enhancers. We conclude that grammar of gene control regions is pervasively used in the patterning of the Drosophila embryo.