Gene regulatory networks and craniofacial patterning in the chick

几个世纪以来，了解地球上生命的多样性及其起源一直占据着人类的思维。事实上，对生物多样性和新类型有机体起源的思考，对于一个能够在生命的各种形式中调和自己的位置的物种来说，具有深远的意义。现代进化发育生物学的一个关键见解是，总的来说，进化是通过基因调控而不是通过基因本身的调控来进行的。因此，识别模式生物基因组中的调控序列，了解它们是如何调控基因表达的，以及它们在不同动物谱系中是如何变化的，是我们重建宏观进化途径的最佳途径。我的研究项目集中在DLX基因(一个由六个相关转录因子组成的家族)的作用机制以及它们对进化多样性的贡献。这些基因本身在动物物种中高度保守，它们在不同动物的大脑、四肢、骨骼和皮肤中以保守的方式发挥作用。我的研究小组探索了在各种胚胎环境中的DLX基因，最近的研究是在颌骨模式中。在小鼠和斑马鱼中DLX基因的实验丢失，以及在人类中自然发生的突变，证实了DLX基因在非常不同种类的脊椎动物的颌骨模式中发挥着保守的作用，并表明它们可能参与了所有脊椎动物颌骨模式的基因调控网络。我们建议从三个方面提高我们对颌骨发育和进化的认识，最初的焦点是DLX基因。我们想要测试小鼠中受DLX调控的候选基因是否直接受到鸡胚中DLX转录因子的调控，如果是的话，什么DNA序列介导了这一调控。此外，我们将以一种公正的方式确定DLX蛋白在鸡胚胎颌骨形成组织中的新的基因组结合位点，从而确定受这些序列调控的基因。我们对这些调控元素在两个不同时间尺度上的功能感兴趣。一方面，我们想从分子细节上了解这些元素在单个鸡胚胎发育中的作用。另一方面，我们希望比较不同种类的脊椎动物之间的调控网络的相似和不同，以了解这些网络是如何随着进化时间的推移而变化的。对于后一个目标，我们将操纵这些调控元件的序列，以了解它们如何在鸡的基因表达调控中发挥作用，并询问这与它们在小鼠身上的功能是相同还是不同。这项研究将促进我们在一个重要的模式系统(雏鸡)中的颌骨发育和更广泛的基因调控方面的知识。这项工作还将产生新的工具来改进鸡胚中的基因功能操作，这可能会使加拿大家禽业受益。

Understanding the diversity of life on earth, and its origins, has occupied human thought for centuries. Indeed, contemplation of biological diversity and the origins of novel types of organisms is deeply significant for a species capable of reconciling its own place in life's great variety of forms. A key insight of modern evolutionary developmental biology is that, by and large, evolution proceeds through modulation of gene regulation, rather than by modulation of the genes themselves. Identifying regulatory sequences in the genomes of model organisms, understanding how they operate to regulate gene expression, and how they have changed in different animal lineages is, therefore, our best way to reconstruct pathways of macroevolution. My research program focuses on the mechanisms of action of Dlx genes (a family of six related transcription factors) and their contributions to evolutionary diversity. The genes themselves are highly conserved across animal species and they function in conserved ways in the brain, limbs, skeleton, and skin of diverse kinds of animals. My research group explores Dlx genes in a variety of these embryonic contexts, most recently in jaw patterning. Experimental loss of Dlx genes in mice and zebrafish, and naturally occurring mutations in humans, confirm that Dlx genes play a conserved role in jaw patterning in very different kinds of vertebrates and point to the likelihood that they participate in regulatory networks of genes that pattern jaws in all vertebrates. We propose to advance our knowledge of jaw development and evolution on three fronts, with Dlx genes as the initial focus. We want to test whether candidate Dlx-regulated genes in mice are directly regulated by Dlx transcription factors in the chick embryo and, if so, what DNA sequences mediate that regulation. Additionally we will identify, in an unbiased way, novel genome binding sites for Dlx proteins in jaw forming tissue in chick embryos and, thereby, the genes regulated by those sequences. We are interested in the functions of these regulatory elements on two different timescales. On the one hand, we want to understand how those elements function in individual chick embryo development in molecular detail. On the other hand, we wish to compare how the regulatory networks are similar and different among diverse kinds of living vertebrates to understand how the networks have changed over evolutionary time. For the latter objective, we will manipulate the sequences of these regulatory elements to understand how they function in the regulation of gene expression in the chick, and ask whether this is the same or different from their functions in mice. This research will advance our knowledge of jaw development in an important model system (the chick) and of gene regulation more broadly. This work will also generate novel tools to improve gene function manipulation in the chicken embryo, which may benefit the Canadian poultry industry.