Department of Developmental and Cell Biology, University of California Irvine, USA.
Center for Complex Biological Systems, University of California Irvine, USA.
Genome Biol Evol. 2021 Dec 1;13(12). doi: 10.1093/gbe/evab221.
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. 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-h head regeneration and 72-h 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 the organism body or regenerating tissue. We used histone modification ChIP-seq to identify 9,998 candidate proximal promoter and 3,018 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.
刺胞动物模式生物水螅因其头部再生的显著能力而长期受到研究，头部由位于口盘附近的头部组织者控制。经典 Wnt 途径在头部组织者功能的再生和芽形成中起着核心作用，芽形成是水螅的无性繁殖方式。然而，在芽形成和再生中，头部组织者发生的发育程序共享程度尚不清楚。头部再生和芽形成过程中基因表达变化的时间序列分析揭示了在 48 小时头部再生和 72 小时芽形成过程中，有一组 298 个差异表达基因。为了了解控制水螅头部再生的调控元件，我们首先鉴定了 27,137 个开放染色质元件，这些元件在生物体或再生组织的一个或多个部分中是开放的。我们使用组蛋白修饰 ChIP-seq 分别鉴定了 9,998 个候选近端启动子和 3,018 个候选增强子样区域。我们表明，这些调控元件的一部分在头部再生过程中是动态重塑的，并确定了一组在头部再生过程中激活的增强子区域中富集的转录因子基序。我们的研究结果表明，水螅显示出发育动态增强子的复杂基因调控结构，这表明复杂发育增强子的进化发生在刺胞动物和两侧对称动物的分化之前。
