Evolution of GRN for Novelty

这一建议试图了解基因组(生物的总DNA序列)如何进化以产生动物形状的多样性。在对许多动物的基因组进行分析之前，人们认为动物的发育是不同的，因为它们拥有不同的蛋白质编码基因。现在人们意识到，即使是非常不同的动物也有相似的一组基因，导致差异的不是基因本身，而是它们在胚胎发育过程中的使用方式。然而，人们对这些基因在发育过程中的不同使用方式知之甚少，这对于理解动物在进化过程中可能发生的形状变化类型很重要。这一建议利用了一组进化出新功能的基因的一个明显例子，即在海胆中形成幼虫骨架，而大多数棘皮动物(包括海胆在内的群体)只在成年动物中形成骨架。基因调控的哪些变化导致了这种基本的新能力？将生成许多社区资源，包括将在公共数据库(如NCBI和Echinobase)上共享的DNA序列。这项提议还将培训博士后研究人员、研究生和本科生，包括那些来自传统上在科学界代表性不足的群体的人。更广泛的公众也将通过卡内基梅隆大学奥舍终身学习学院的一系列公开讲座以及与当地K-12公立学校的外联计划参与这项研究。海胆幼体骨骼发育的基因调控网络(GRN)是众所周知的。其他类外棘皮动物的幼虫没有或非常少的幼虫骨骼，但所有的棘皮动物都在变态后形成骨骼。先前的证据表明，海胆幼虫的骨骼是从GRN中挑选出来的，用于形成这个成年骨骼。这项提议的第一个目标是确定从成人骨骼发育计划中增选出来的、在海星中胚层中不同表达的基因集，海星中胚层不形成骨骼。差异RNA-Seq将用于筛选海胆、海参和海星中的潜在基因。整装原位杂交将用于确定它们的空间位置。下一个目标是了解顺式调节模块(CRM)如何在新的幼虫环境中发挥作用，并了解幼体海胆中增选基因亚电路的功能。ChIP-Seq将识别CRM及其相关基因。CRM的功能解剖和识别的共享靶标基因的扰动将决定这些CRM如何在原始和新电路中发挥作用，以及允许共选的反式环境的类型和子电路拓扑结构。这项工作将有助于理解GRN的可塑性和进化性。

This proposal seeks to understand how genomes (the total DNA sequences of a creature) evolve to generate diversity in animal shapes. Prior to the analysis of genomes of many animals, it was assumed that animals developed differently because they had different protein-coding genes. It is now realized that even very different animals have similar sets of genes, and it is not the genes themselves, but how they are used during embryonic development, that lead to differences. How those genes are used differently during development is poorly understood, however, and is important for understanding the types of changes in animal shape that can occur during evolution. This proposal takes advantage of a clear example of a set of genes that have evolved a new function, i.e. to make a larval skeleton in the sea urchin, while most echinoderms (the group that includes the sea urchins) make a skeleton only in the adult animal. What changes in gene regulation led to this basic new ability? Many community resources will be generated including DNA sequences that will be shared on publically available databases such as NCBI and Echinobase. This proposal will also train postdoctoral researchers, graduate students, and undergraduates, including those from groups that are traditionally underrepresented in science. The broader public will also be engaged in this research through a series of public lectures in Carnegie Mellon's Osher Lifelong Learning Institute and through outreach programs with local K-12 public schools. The gene regulatory network (GRN) for the development of the sea urchin larval skeleton is very well known. Other out-group echinoderm larvae have no or very reduced larval skeletons, yet all echinoderms make a skeleton after metamorphosis. Prior evidence suggests that the sea urchin larval skeleton was co-opted from the GRN for the formation of this adult skeleton. The first objective of this proposal is to determine the set of genes that have been co-opted from the adult skeletogenic program, and are differently expressed in the sea star mesoderm, which does not form a skeleton. Differential RNA-Seq will be used to screen for potential genes in sea urchin, sea cucumbers, and a sea star. Whole-mount in situ hybridization will be used to determine their spatial location. The next objective is to understand how cis-regulatory modules (CRMs) can function in the new larval context and to understand the function of the subcircuits of the co-opted genes in larval sea urchins. ChIP-Seq will identify CRMs and their associated genes. Functional dissection of CRMs and perturbation of identified target genes that are shared targets will determine how these CRMs can function in both the original and new circuit, and also the types of trans environments, and subcircuit topologies that permit cooption. This work will contribute to an understanding of the plasticity and evolvability of GRNs.