Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila [ATAC-seq]

The loss of discrete morphological traits, the most common evolutionary transition, is typically driven by changes in expression of developmental genes. Mutations accumulating in regulatory elements of these genes can disrupt DNA binding sites for transcription factors patterning their spatial expression, or delete entire enhancers. Regulatory elements, however, may in principle be silenced through other mechanisms, including changes in chromatin accessibility, or the emergence of repressive elements. Here, we show that an increase in chromatin accessibility at the pigmentation gene yellow, combined with the gain of a repressor site, underlie the evolutionary loss of a spot pigmentation pattern on the wings of a Drosophila species. The evolutionary gain of accessibility of this repressive element is regulated by E93, a transcription factor governing the progress of metamorphosis. This convoluted evolutionary scenario contrasts with the classical parsimonious mutational paths generally envisioned and often documented for morphological losses. It illustrates for the first time how evolutionary changes in chromatin accessibility may directly contribute to morphological diversification. We profiled chromatin accessibility at selected stages in the pupal wings of D. melanogaster and D. biarmipes using ATAC-seq. Chromatin accessibility was profiled at five time points during pupal development based on the expression dynamics of yellow in the wings of both species. The five time points include: 0%, 48%, 60%, 69%, and 78% of pupal development. Two biological replicates were prepared for each stage.