We used capped analysis of gene expression with sequencing (CAGE-seq) to profile eRNA expression and enhancer activity during embryogenesis of a model echinoderm: the sea urchin, Strongylocentrotus purpuratus. We identified more than 18,000 enhancers that were active in mature oocytes and developing embryos and documented a burst of enhancer activation during cleavage and early blastula stages. We found that a large fraction (73.8%) of all enhancers active during the first 48 h of embryogenesis were hyperaccessible no later than the 128-cell stage and possibly even earlier. Most enhancers were located near gene bodies, and temporal patterns of eRNA expression tended to parallel those of nearby genes. Furthermore, enhancers near lineage-specific genes contained signatures of inputs from developmental gene regulatory networks deployed in those lineages. A large fraction (60%) of sea urchin enhancers previously shown to be active in transgenic reporter assays was associated with eRNA expression. Moreover, a large fraction (50%) of a representative subset of enhancers identified by eRNA profiling drove tissue-specific gene expression in isolation when tested by reporter assays. Our findings provide an atlas of developmental enhancers in a model sea urchin and support the utility of eRNA profiling as a tool for enhancer discovery and regulatory biology. The data generated in this study are available at Echinobase, the public database of information related to echinoderm genomics.

中文翻译：

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通过 eRNA 分析评估海胆胚胎发生过程中增强子活性的全球模式

我们使用测序基因表达的封顶分析 (CAGE-seq) 来分析模型棘皮动物胚胎发生过程中的 eRNA 表达和增强子活性：海胆、Strongylocentrotus purpuratus. 我们确定了 18,000 多个在成熟卵母细胞和发育中的胚胎中活跃的增强子，并记录了在卵裂和早期囊胚阶段增强子激活的爆发。我们发现，在胚胎发生的前 48 小时内活跃的所有增强子中的很大一部分（73.8%）在不迟于 128 细胞阶段甚至可能更早之前是超易接近的。大多数增强子位于基因体附近，并且 eRNA 表达的时间模式倾向于与附近基因的时间模式平行。此外，靠近谱系特异性基因的增强子包含来自部署在这些谱系中的发育基因调控网络的输入信号。大部分 (60%) 的海胆增强剂先前显示在转基因报告分析中具有活性，这与 eRNA 表达有关。而且，当通过报告基因分析测试时，通过 eRNA 分析鉴定的增强子的代表性子集的很大一部分（50%）单独驱动组织特异性基因表达。我们的研究结果提供了模型海胆中发育增强子的图谱，并支持 eRNA 分析作为增强子发现和调控生物学工具的效用。本研究生成的数据可在 Echinobase 获取，该数据库是与棘皮动物基因组学相关的公共信息数据库。