Unique establishment of procephalic head segments is supported by the identification of cis-regulatory elements driving segment-specific segment polarity gene expression in Drosophila

Anterior head segmentation is governed by different regulatory mechanisms than those that control trunk segmentation in Drosophila. For segment polarity genes, both initial mode of activation as well as cross-regulatory interactions among them differ from the typical genetic circuitry in the trunk and are unique for each of the procephalic segments. In order to better understand the segment-specific gene network responsible for the procephalic expression of the earliest active segment polarity genes wingless and hedgehog, we started to identify and analyze cis-regulatory DNA elements of these genes. For hedgehog, we could identify a cis-regulatory element, ic-CRE, that mediates expression specifically in the posterior part of the intercalary segment and requires promoter-specific interaction for its function. The intercalary stripe is the last part of the metameric hedgehog expression pattern that appears during embryonic development, which probably reflects the late and distinct establishment of this segment. The identification of a cis-regulatory element that is specific for one head segment supports the mutant-based observation that the expression of segment polarity genes is governed by a unique gene network in each of the procephalic segments. This provides further indication that the anterior-most head segments represent primary segments, which are set up independently, in contrast to the secondary segments of the trunk, which resemble true repetitive units.

Protocol publication

[…] In silico analysis to identify putative transcription factor binding sites within cis-regulatory regions was performed using the MatInspector (Cartharius et al. ; http://www.genomatix.de/online_help/help_matinspector/matinspector_help.html; http://www.genomatix.de/cgi-bin/matinspector_prof/mat_fam.pl). Predictions were inspected manually, checked in correlation with literature reports, and filtered through phylogenetic conservation using the Drosophila EvoPrinter (http://evoprinter.ninds.nih.gov/evoprintprogramHD/evphd.html) or the UCSC Genome Browser (http://genome.ucsc.edu/cgi-bin/hgGateway). […]