Enhancer evolution in chordates: Lessons from functional analyses of cephalochordate cis-regulatory modules.,Development, Growth & Differentiation

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Enhancer evolution in chordates: Lessons from functional analyses of cephalochordate cis-regulatory modules.
Development, Growth & Differentiation ( IF 1.7 ) Pub Date : 2020-06-01 , DOI: 10.1111/dgd.12684
Yuuri Yasuoka ₁

Affiliation

Chordates comprise three major groups, cephalochordates (amphioxus), tunicates (urochordates), and vertebrates. Since cephalochordates were the early branching group, comparisons between amphioxus and other chordates help us to speculate about ancestral chordates. Here, I summarize accumulating data from functional studies analyzing amphioxus cis‐regulatory modules (CRMs) in model systems of other chordate groups, such as mice, chickens, clawed frogs, fish, and ascidians. Conservatism and variability of CRM functions illustrate how gene regulatory networks have evolved in chordates. Amphioxus CRMs, which correspond to CRMs deeply conserved among animal phyla, govern reporter gene expression in conserved expression domains of the putative target gene in host animals. In addition, some CRMs located in similar genomic regions (intron, upstream, or downstream) also possess conserved activity, even though their sequences are divergent. These conservative CRM functions imply ancestral genomic structures and gene regulatory networks in chordates. However, interestingly, if expression patterns of amphioxus genes do not correspond to those of orthologs of experimental models, some amphioxus CRMs recapitulate expression patterns of amphioxus genes, but not those of endogenous genes, suggesting that these amphioxus CRMs are close to the ancestral states of chordate CRMs, while vertebrates/tunicates innovated new CRMs to reconstruct gene regulatory networks subsequent to the divergence of the cephalochordates. Alternatively, amphioxus CRMs may have secondarily lost ancestral CRM activity and evolved independently. These data help to solve fundamental questions of chordate evolution, such as neural crest cells, placodes, a forebrain/midbrain, and genome duplication. Experimental validation is crucial to verify CRM functions and evolution.

中文翻译：

增强器在脊索动物中的进化：从头孢酸盐顺式调节模块的功能分析中获得的经验教训。

脊索动物包括三大类，头针动物（amphioxus），被膜动物（urochordates）和脊椎动物。由于头孢类是早期的分支类，因此，对两栖类和其他类的比较可以帮助我们推测出祖类类。在这里，我总结了功能研究中积累的数据，这些研究分析了其他诸如猪，鸡，有爪蛙，鱼和海鞘等其他碳酸盐类动物模型系统中的两性顺式调节模块（CRM）。CRM功能的保守性和可变性说明了基因调控网络是如何在进化过程中进化的。Amphioxus CRMs对应于在动物门中非常保守的CRM，它在宿主动物的假定靶基因的保守表达域中控制报告基因的表达。此外，一些CRM位于相似的基因组区域（内含子，上游，或下游）也具有保守的活性，即使它们的序列是不同的。这些保守的CRM功能暗示着脊索动物的祖先基因组结构和基因调控网络。然而，有趣的是，如果两栖动物基因的表达模式与实验模型的直系同源基因不匹配，则某些两栖动物CRM会概括两栖动物基因的表达模式，而不是内源基因的表达模式，这表明这些两栖动物CRM都接近祖先状态。脊索动物CRM，而脊椎动物/被膜类动物创新了新的CRM，以在头领动物发散后重建基因调控网络。或者，两栖类CRM可能会继而失去祖先CRM活动并独立发展。这些数据有助于解决胆酸盐进化的基本问题，例如神经c细胞，斑块，前脑/中脑和基因组重复。实验验证对于验证CRM功能和演进至关重要。

更新日期：2020-06-29

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