The epithelial and interstitial stem cells of the freshwater polyp Hydra are the best-characterized stem cell systems in any cnidarian, providing valuable insight into cell type evolution and the origin of stemness in animals. However, little is known about the transcriptional regulatory mechanisms that determine how these stem cells are maintained and how they give rise to their diverse differentiated progeny. To address such questions, a thorough understanding of transcriptional regulation in Hydra is needed. To this end, we generated extensive new resources for characterizing transcriptional regulation in Hydra, including new genome assemblies for Hydra oligactis and the AEP strain of Hydra vulgaris, an updated whole-animal single-cell RNA-seq atlas, and genome-wide maps of chromatin interactions, chromatin accessibility, sequence conservation, and histone modifications. These data revealed the existence of large kilobase-scale chromatin interaction domains in the Hydra genome that contain transcriptionally coregulated genes. We also uncovered the transcriptomic profiles of two previously molecularly uncharacterized cell types: isorhiza-type nematocytes and somatic gonad ectoderm. Finally, we identified novel candidate regulators of cell type–specific transcription, several of which have likely been conserved at least since the divergence of Hydra and the jellyfish Clytia hemisphaerica more than 400 million years ago.

中文翻译：

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水螅基因组的染色体规模表观遗传图谱揭示了细胞状态的保守调节因子


淡水息肉水螅的上皮干细胞和间质干细胞是所有刺胞动物中特征最鲜明的干细胞系统，为了解细胞类型进化和动物干性起源提供了宝贵的见解。然而，人们对决定这些干细胞如何维持以及如何产生多样化分化后代的转录调控机制知之甚少。为了解决这些问题，需要彻底了解水螅的转录调控。为此，我们生成了广泛的新资源来表征水螅的转录调控，包括寡水螅和普通水螅的 AEP 菌株的新基因组组装、更新的全动物单细胞 RNA-seq 图谱以及染色质相互作用、染色质可及性、序列保守性和组蛋白修饰。这些数据揭示了水螅基因组中存在大型千碱基级染色质相互作用域，其中包含转录共调控基因。我们还发现了两种以前分子上未表征的细胞类型的转录组谱：异根型线虫细胞和体细胞性腺外胚层。最后，我们确定了细胞类型特异性转录的新候选调节因子，其中一些调节因子可能至少自 4 亿多年前水螅和水母Clytia hemisphaerica分化以来就一直保守。