RNA profiling has provided increasingly detailed knowledge of gene expression patterns, yet the different regulatory architectures that drive them are not well understood. To address this, we profiled and compared transcriptional and regulatory element activities across five tissues of Caenorhabditis elegans, covering ∼90% of cells. We find that the majority of promoters and enhancers have tissue-specific accessibility, and we discover regulatory grammars associated with ubiquitous, germline, and somatic tissue–specific gene expression patterns. In addition, we find that germline-active and soma-specific promoters have distinct features. Germline-active promoters have well-positioned +1 and −1 nucleosomes associated with a periodic 10-bp WW signal (W = A/T). Somatic tissue–specific promoters lack positioned nucleosomes and this signal, have wide nucleosome-depleted regions, and are more enriched for core promoter elements, which largely differ between tissues. We observe the 10-bp periodic WW signal at ubiquitous promoters in other animals, suggesting it is an ancient conserved signal. Our results show fundamental differences in regulatory architectures of germline and somatic tissue–specific genes, uncover regulatory rules for generating diverse gene expression patterns, and provide a tissue-specific resource for future studies.

中文翻译：

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线虫中生殖系活性基因和体细胞基因的独特调控结构

RNA 分析提供了越来越详细的基因表达模式的知识，但驱动它们的不同监管架构尚不清楚。为了解决这个问题，我们分析并比较了秀丽隐杆线虫五种组织的转录和调节元件活性，覆盖约 90% 的细胞。我们发现大多数启动子和增强子具有组织特异性的可及性，并且我们发现了与普遍存在的、生殖系和体细胞组织特异性基因表达模式相关的调控语法。此外，我们发现种系活性和体细胞特异性启动子具有不同的特征。种系活性启动子具有定位良好的 +1 和 -1 核小体，与周期性 10 bp WW 信号 (W = A/T) 相关。体细胞组织特异性启动子缺乏定位的核小体和这种信号，具有广泛的核小体耗尽区域，并且更富含核心启动子元件，这些元件在组织之间有很大差异。我们观察到其他动物普遍存在的启动子处的 10 bp 周期性 WW 信号，表明它是一个古老的保守信号。