Background Mutations in gene regulatory networks often lead to genetic divergence without impacting gene expression or developmental patterning. The rules governing this process of developmental systems drift, including the variable impact of selective constraints on different nodes in a gene regulatory network, remain poorly delineated. Results Here we examine developmental systems drift within the cardiopharyngeal gene regulatory networks of two tunicate species, Corella inflata and Ciona robusta. Cross-species analysis of regulatory elements suggests that trans-regulatory architecture is largely conserved between these highly divergent species. In contrast, cis-regulatory elements within this network exhibit distinct levels of conservation. In particular, while most of the regulatory elements we analyzed showed extensive rearrangements of functional binding sites, the enhancer for the cardiopharyngeal transcription factor FoxF is remarkably well-conserved. Even minor alterations in spacing between binding sites lead to loss of FoxF enhancer function, suggesting that bound trans-factors form position-dependent complexes. Conclusions Our findings reveal heterogeneous levels of divergence across cardiopharyngeal cis-regulatory elements. These distinct levels of divergence presumably reflect constraints that are not clearly associated with gene function or position within the regulatory network. Thus, levels of cis-regulatory divergence or drift appear to be governed by distinct structural constraints that will be difficult to predict based on network architecture.

中文翻译：

---

被囊动物心咽基因调控元件的漂移水平不同。

背景 基因调控网络的突变通常会导致遗传分歧，但不会影响基因表达或发育模式。控制发育系统漂移过程的规则，包括基因调控网络中不同节点的选择性约束的可变影响，仍然缺乏明确的描述。结果在这里，我们检查了两种被囊类动物（Corella inflata 和 Ciona RObsta）心咽基因调控网络内的发育系统漂移。对调控元件的跨物种分析表明，跨调控结构在这些高度分化的物种之间很大程度上是保守的。相比之下，该网络内的顺式调控元件表现出不同程度的保守性。特别是，虽然我们分析的大多数调控元件显示功能结合位点的广泛重排，但心咽转录因子 FoxF 的增强子却非常保守。即使结合位点之间的间距发生微小变化也会导致 FoxF 增强子功能丧失，这表明结合的反式因子形成位置依赖性复合物。结论 我们的研究结果揭示了心咽顺式调节元件之间的差异程度不同。这些不同水平的分歧可能反映了与基因功能或调控网络中的位置没有明确关联的限制。因此，顺式监管分歧或漂移的水平似乎受到不同的结构约束的控制，而这些结构约束很难根据网络架构进行预测。