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.

昆虫躯体构型的关键演化创新与特有新生器官，推动了其对新生境的卓越适应能力，促进了该类群的辐射演化。为阐明这些新生结构的起源与演化机制，亟需解析参与昆虫胚胎发育过程的基因及基因调控网络。尽管学界已从基因表达与调控的视角，对全变态昆虫（尤其是黑腹果蝇Drosophila melanogaster）的发育机制开展了大量深入研究，但半变态昆虫的发育过程，以及调控其胚胎发生的基因表达与调控动态，仍未得到充分解析。因此，本研究旨在探究半变态昆虫——蜉蝣Cloeon dipterum（隶属于古翅类蜉蝣目Ephemeroptera，是所有其他有翅昆虫的姊妹群）发育过程中的基因调控动态。为此，我们首次在蜉蝣中应用ATAC-seq（转座酶可及性测序，Assay for transposase-Accessible Chromatin using sequencing）技术，选取其胚胎发育的6个不同时间节点，鉴定出对应于通用及阶段特异性启动子与增强子的染色质可及区域。通过这套综合数据集，我们揭示了胚胎发育第8至10阶段间染色质可及性的显著变化，该阶段对应腹部分节、器官发生及附肢发育过程。本研究在蜉蝣中应用ATAC-seq技术，有助于解析半变态昆虫胚胎发育的表观遗传机制，同时将为理解有翅昆虫的基因调控演化提供重要基础资源。