Evolution of GRN for Novelty

该提案旨在了解基因组（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具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。 这一提议利用了一组基因的明显例子，这些基因已经进化出一种新的功能，即在海胆中制造幼虫骨架，而大多数棘皮动物（包括海胆的群体）只在成年动物中制造骨架。 是什么基因调控的变化导致了这种基本的新能力？ 将产生许多社区资源，包括将在NCBI和Echinobase等医学可用数据库上共享的DNA序列。 这项提案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领域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。 其他外群棘皮动物的幼虫没有或非常少的幼虫骨骼，但所有棘皮动物在变态后都有骨骼。 先前的证据表明，海胆幼虫骨骼是从GRN中挑选出来的，用于形成这具成年骨骼。 这项建议的第一个目标是确定一组基因，这些基因是从成体骨骼发育程序中选出的，并且在不形成骨骼的海星星星中胚层中表达不同。 差异RNA-Seq将用于筛选海胆、海参和一颗海星星星中的潜在基因。 将使用整体原位杂交来确定其空间位置。 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，并了解幼虫海胆中增选基因的子电路的功能。 ChIP-Seq将识别CRM及其相关基因。 标准物质的功能解剖和干扰的共同目标的确定的靶基因将确定这些标准物质如何可以在原始和新的电路，以及类型的反式环境，和子电路拓扑结构，允许cooption。 这项工作将有助于理解的可塑性和进化的GRN。

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.