The regulation of Hox genes by microRNAs during Drosophila development

Hox genes encode a family of evolutionarily conserved transcription factors involved in the activation of diverse cell differentiation programs along the antero-posterior axis of animals. Hox gene expression is controlled by a complex set of regulatory mechanisms which are still not fully understood. Despite this, misregulation of Hox gene expression can lead to severe developmental abnormalities and various forms of disease. This work addresses the way in which small non-coding RNAs (microRNAs, miRNAs) regulate Hox gene expression and function during development. To do this we use the Drosophila Hox gene Ultrabithorax (Ubx) as a paradigm for Hox gene function. Using a suite of genetic methods we first uncover a novel regulatory interaction between Drosophila Ubx and the miR-310C family of miRNAs during the development of the haltere, a small dorsal appendage involved in flight control. We also show that this miRNA cluster is required to fine tune Ubx expression. Furthermore, our data provides insight into the role played by Ubx during appendage development. Secondly, using a next generation RNA sequencing approach, we identify the full repertoire of miRNAs present in two serially homologous appendages of Drosophila – the wing and haltere. Our results show that these morphologically distinct appendages have divergent miRNA profiles, including miRNAs which display appendage-specific expression patterns. In addition, combining these profiles with available transcriptomic data enabled us to study how miRNAs are integrated into the Ubx gene regulatory networks that govern haltere development. This analysis suggests that haltere miRNAs reinforce the regulatory programmes installed by Ubx during haltere development. Our work therefore contributes to the understanding of the regulatory function of miRNAs during development and sheds light on the ways in which Hox gene expression can contribute to the formation of complex morphological structures.