Data from: Geometric control of ciliated band regulatory states in the sea urchin embryo

The trapezoidal ciliated band (CB) of the postgastrular sea urchin embryo surrounds the oral ectoderm, separating it from adjacent embryonic territories. Once differentiated, the CB is composed of densely arranged cells bearing long cilia that endow the larva with locomotion and feeding capability. The spatial pattern from which the CB will arise is first evidenced during pregastrular stages by expression of the pioneer gene onecut. Immediately after gastrulation, the CB consists of four separate regulatory state domains, each of which express a unique set of transcription factors. These are: (1) The oral apical CB, located within the apical neurogenic field; (2) The animal lateral CB, which bilaterally separates the oral from aboral ectoderm; (3) The vegetal lateral CB, which bilaterally serves as signaling centers; and (4) The vegetal oral CB, which delineates the boundary with the underlying endoderm. Remarkably, almost all of the regulatory genes specifically expressed within these domains are down-regulated by interference with Soxb1 expression, implying activation by this factor in common. In this work we show how the boundaries of the CB subdomains are established, and thus ascertain the design principle by which the geometry of this unique and complex regulatory state pattern is genomically controlled. Each of these boundaries, on either side of the CB, is defined by spatially confined transcriptional repressors, the products of regulatory genes operating across the border of each subdomain. In total, this requires deployment of about ten different repressors, which we identify in this work, thus exemplifying the high informational requirement of spatial regulatory organization during embryogenesis.

原肠后期海胆胚胎的梯形纤毛带（trapezoidal ciliated band, CB）环绕口腔外胚层，将其与相邻胚胎区域相互分隔。当CB完成分化后，其由密集排列的长纤毛细胞构成，可为幼虫提供运动与摄食的能力。CB的前体空间模式最早可在原肠胚前期（pregastrular stages）通过先驱基因onecut的表达得以显现。原肠作用（gastrulation）刚完成时，CB已形成四个独立的调控状态结构域，每个结构域均表达一套独特的转录因子，具体如下：(1) 口顶端CB，定位于顶端神经发生区；(2) 动物极侧CB，双侧分隔口腔外胚层与反口外胚层；(3) 植物极侧CB，双侧作为信号中心发挥功能；(4) 口植物极侧CB，划定与下方内胚层的边界。值得注意的是，几乎所有在这些结构域中特异性表达的调控基因，在Soxb1表达受到干扰时均会出现下调，暗示该因子对这些基因存在共同激活作用。本研究阐明了CB亚结构域边界的建立机制，并由此揭示了这种独特且复杂的调控状态模式的几何结构在基因组层面的调控设计原则。CB两侧的每一处边界，均由空间限制性转录抑制因子所定义——这些抑制因子是在各亚结构域边界处行使功能的调控基因的表达产物。本研究共鉴定出约十种不同的抑制因子，以此例证了胚胎发生过程中空间调控组织所具有的极高信息需求。