Gene regulatory dynamics during the development of a paleopteran insect, the mayfly Cloeon dipterum
The key evolutionary innovations in the body plan and specific novel organs of insects promoted their outstanding ability to adapt to new habitats and boosted the radiation of the lineage. To understand the origin and evolution of these new structures, t is essential to investigate which are the genes and gene regulatory networks which participate during the embryonic development of insects. Although great efforts have been made to fully understand, from a gene expression and gene regulation point of view, the development of holometabolous insects, in particular, Drosophila melanogaster, how hemimetabolous insects develop, and which are the dynamics of gene expression and gene regulation that control their embryogenesis, are still poorly characterized. Therefore, we aimed at understanding the gene regulation dynamics during the development of an hemimetabolous insect, the mayfly Cloeon dipterum, which belongs to the paleopteran order of Ephemeroptera, the sister group to all other winged insects. For this, we applied ATAC-seq (Assay for transposase-Accessible Chromatin using sequencing), for the first time in mayflies, at six different time points of its embryonic development and identify accessible chromatin regions corresponding to both general and stage-specific promoters and enhancers. With these comprehensive datasets, we reported pronounced changes in accessible chromatin between stages 8 and 10 of embryonic development, which correspond to the segmentation of the abdomen, organogenesis, and development of appendixes. The application of ATAC-seq in mayflies has contributed to identify the epigenetic mechanisms responsible for embryonic development in hemimetabolous insects and it will provide a fundamental resource to understand the evolution of gene regulation in winged insects.