Integrative analysis of Hydra head regeneration reveals activation of distal enhancer-like elements [ATAC-seq]

The cnidarian model organism Hydra has long been studied for its remarkable ability to regenerate its head, which is controlled by a head organizer located near the hypostome. Cnidarians and bilaterians diverged about 600 millions years ago but the gene contents of species of both phyla are surprisingly similar despite divergent morphologies and functions. While little is known about the role of cis-regulatory elements in cnidarians, understanding gene regulatory mechanisms in cnidarians can potentially shed light on metazoan evolution. The canonical Wnt pathway plays a central role in head organizer function during regeneration and during bud formation, which is the asexual mode of reproduction in Hydra. However, it is unclear how shared the developmental programs of head organizer genesis are in budding and regeneration. Time-series analysis of gene expression changes during head regeneration and budding revealed a set of 298 differentially expressed genes during the 48-hour head regeneration and 72-hour budding time-courses. In order to understand the regulatory elements controlling hydra head regeneration, we first identified 27,137 open-chromatin elements that are open in one or more sections of organism. We used histone modification ChIP-seq to identify 9998 candidate proximal promoter and 3018 candidate enhancer-like regions respectively. We show that a subset of these regulatory elements is dynamically remodeled during head regeneration and identify a set of transcription factor motifs that are enriched in the enhancer regions activated during head regeneration. Our results show that Hydra displays complex gene regulatory structures of developmentally dynamic enhancers, which suggests that the evolution of complex developmental enhancers predates the split of cnidarians and bilaterians.

刺胞动物（cnidarian）模式生物水螅长期以来因其卓越的头部再生能力而被广泛研究，其头部再生由位于口锥附近的头部组织者调控。刺胞动物与两侧对称动物约在6亿年前发生分化，尽管二者形态与功能存在显著分歧，两个类群的物种基因组成却惊人相似。目前学界对刺胞动物顺式调控元件（cis-regulatory elements）的功能认知仍较为有限，但解析刺胞动物的基因调控机制，或可为后生动物（metazoan）的演化研究提供重要洞见。经典Wnt通路（canonical Wnt pathway）在水螅头部再生及出芽（水螅的无性繁殖方式）过程中的头部组织者功能中发挥核心作用。然而，目前尚不清楚出芽与再生过程中的头部组织者发生的发育程序共享程度如何。对头部再生和出芽过程中的基因表达变化进行时序分析后，研究团队分别在48小时头部再生和72小时出芽的时序进程中，鉴定出298个差异表达基因（differentially expressed genes）。为解析调控水螅头部再生的调控元件，本研究首先鉴定出27137个在生物体一个或多个区域处于开放状态的开放染色质元件（open-chromatin elements）；随后通过组蛋白修饰染色质免疫共沉淀测序（histone modification ChIP-seq），分别鉴定出9998个候选近端启动子（proximal promoter）区域与3018个候选类增强子区域（enhancer-like regions）。本研究证实，其中一类调控元件在头部再生过程中发生动态重塑，并鉴定出在头部再生激活的增强子区域中富集的一组转录因子基序（transcription factor motifs）。研究结果表明，水螅具备发育动态调控的复杂基因调控增强子结构，这提示复杂发育增强子的演化早于刺胞动物与两侧对称动物的分化事件。