A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait

Abstract

Animal traits develop through the expression and action of numerous regulatory and realizator genes that comprise a gene regulatory network (GRN). For each GRN, its underlying patterns of gene expression are controlled bycis-regulatory elements (CREs) that bind activating and repressing transcription factors. These interactions drive cell-type and developmental stage-specific transcriptional activation or repression. Most GRNs remain incompletely mapped, and a major barrier to this daunting task is CRE identification. Here, we used anin silicomethod to identify predicted CREs (pCREs) that comprise the GRN which governs sex-specific pigmentation ofDrosophila melanogaster. Throughin vivoassays, we demonstrate that many pCREs activate expression in the correct cell-type and developmental stage. We employed genome editing to demonstrate that two CREs control the pupal abdomen expression oftrithorax, whose function is required for the dimorphic phenotype. Surprisingly,trithoraxhad no detectable effect on this GRN’s keytrans-regulators, but shapes the sex-specific expression of two realizator genes. Comparison of sequences orthologous to these CREs supports an evolutionary scenario where thesetrithoraxCREs predated the origin of the dimorphic trait. Collectively, this study demonstrates howin silicoapproaches can shed novel insights on the GRN basis for a trait’s development and evolution.