Evolution of GRN for Novelty

这一提议旨在了解基因组（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不同是因为它们有不同的蛋白质编码基因。现在人们认识到，即使是非常不同的动物也有相似的基因组，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如何被不同地使用知之甚少，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。这一提议利用了一个明显的例子，即一组基因进化出了一种新功能，即在海胆中形成幼体骨骼，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骼。基因调控的哪些变化导致了这种基本的新能力？将产生许多社区资源，包括DNA序列，这些DNA序列将在NCBI和Echinobase等公共数据库上共享。该提案还将培训博士后研究人员、研究生和本科生，包括那些传统上在科学领域代表性不足的群体。通过卡内基梅隆大学Osher终身学习研究所的一系列公开讲座以及与当地K-12公立学校的外展项目，更广泛的公众也将参与到这项研究中来。海胆幼体骨骼发育的基因调控网络（GRN）是众所周知的。其他外群棘皮动物的幼虫没有或非常少的幼虫骨骼，但所有的棘皮动物在变态后都有骨骼。先前的证据表明，海胆幼体骨架是从GRN中挑选出来形成成体骨架的。该建议的第一个目标是确定从成体骨骼形成程序中被增选的一组基因，这些基因在海星中胚层（不形成骨骼）中表达不同。差分RNA-Seq将用于筛选海胆、海参和海星的潜在基因。全载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控模块（CRMs）如何在新的幼虫环境中发挥作用，并了解海胆幼虫中增选基因的亚回路的功能。ChIP-Seq将鉴定crm及其相关基因。对crm的功能解剖和对已确定的共享靶标靶基因的扰动将决定这些crm如何在原始和新回路中发挥作用，以及跨环境的类型和允许合作的亚回路拓扑结构。这项工作将有助于理解grn的可塑性和可进化性。

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.