Understanding how regulatory mechanisms evolve is critical for understanding the processes that give rise to novel phenotypes. Snake venom systems represent a valuable and tractable model for testing hypotheses related to the evolution of novel regulatory networks, yet the regulatory mechanisms underlying venom production remain poorly understood. Here, we use functional genomics approaches to investigate venom regulatory architecture in the prairie rattlesnake and identify cis-regulatory sequences (enhancers and promoters), trans-regulatory transcription factors, and integrated signaling cascades involved in the regulation of snake venom genes. We find evidence that two conserved vertebrate pathways, the extracellular signal-regulated kinase and unfolded protein response pathways, were co-opted to regulate snake venom. In one large venom gene family (snake venom serine proteases), this co-option was likely facilitated by the activity of transposable elements. Patterns of snake venom gene enhancer conservation, in some cases spanning 50 million yr of lineage divergence, highlight early origins and subsequent lineage-specific adaptations that have accompanied the evolution of venom regulatory architecture. We also identify features of chromatin structure involved in venom regulation, including topologically associated domains and CTCF loops that underscore the potential importance of novel chromatin structure to coevolve when duplicated genes evolve new regulatory control. Our findings provide a model for understanding how novel regulatory systems may evolve through a combination of genomic processes, including tandem duplication of genes and regulatory sequences, cis-regulatory sequence seeding by transposable elements, and diverse transcriptional regulatory proteins controlled by a co-opted regulatory cascade.

中文翻译：

---

蛇毒基因表达由新的调控结构和多种选择的脊椎动物通路的整合来协调

了解调控机制如何演变对于了解产生新表型的过程至关重要。蛇毒系统代表了一种有价值且易于处理的模型，用于测试与新型监管网络演变相关的假设，但对毒液产生的监管机制仍然知之甚少。在这里，我们使用功能基因组学方法来研究草原响尾蛇的毒液调控结构，并确定顺式调控序列（增强子和启动子）、反式-调节转录因子，以及参与调节蛇毒基因的整合信号级联。我们发现有证据表明两种保守的脊椎动物途径，即细胞外信号调节激酶和未折叠蛋白反应途径，被选为调节蛇毒。在一个大型毒液基因家族（蛇毒丝氨酸蛋白酶）中，转座因子的活性可能促进了这种共同选择。蛇毒基因增强子的保存模式，在某些情况下跨越了 5000 万年的谱系分歧，突出了伴随毒液调控结构演变的早期起源和随后的谱系特异性适应。我们还确定了参与毒液调节的染色质结构特征，包括拓扑相关域和 CTCF 环，它们强调了新染色质结构在重复基因进化出新的调控控制时共同进化的潜在重要性。我们的研究结果提供了一个模型，用于理解新的调控系统如何通过基因组过程的组合进化，包括基因和调控序列的串联复制，通过转座因子播种的顺式调控序列，以及由增选调控级联控制的多种转录调控蛋白。