Center for Reproductive Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
Nat Commun. 2024 Nov 1;15(1):9452. doi: 10.1038/s41467-024-53892-0.
Little is known about how the epigenomic states change during development and evolution in a 3D genome context. Here we use Drosophila pseudoobscura with complex turnover of sex chromosomes as a model to address this, by collecting massive epigenomic and Hi-C data from five developmental stages and three adult tissues. We reveal that over 60% of the genes and transposable elements (TE) exhibit at least one developmental transition of chromatin state. Transitions on specific but not housekeeping enhancers are associated with specific chromatin loops and topologically associated domain borders (TABs). While evolutionarily young TEs are generally silenced, old TEs more often have been domesticated as interacting TABs or specific enhancers. But on the recently evolved X chromosome, young TEs are instead often active and recruited as TABs, due to acquisition of dosage compensation. Overall we characterize how Drosophila epigenomic landscapes change during development and in response to chromosome evolution, and highlight the important roles of TEs in genome organization and regulation.
关于 3D 基因组背景下发育和进化过程中表观基因组状态如何变化，目前知之甚少。在这里，我们使用性染色体复杂易位的果蝇拟暗果蝇作为模型来解决这个问题，从五个发育阶段和三个成年组织中收集了大量的表观基因组和 Hi-C 数据。我们揭示了超过 60%的基因和转座元件（TE）至少表现出一种染色质状态的发育转变。特定而非管家增强子上的转变与特定的染色质环和拓扑相关结构域边界（TAB）相关。虽然进化上年轻的 TE 通常被沉默，但较老的 TE 更经常被驯化作为相互作用的 TAB 或特定的增强子。但在最近进化的 X 染色体上，由于获得了剂量补偿，年轻的 TE 通常更活跃，并被招募为 TAB。总的来说，我们描述了果蝇表观基因组景观在发育过程中以及对染色体进化的响应中的变化，并强调了 TE 在基因组组织和调控中的重要作用。
