Interspecific Conservation of cis-Regulatory Modules: Why It Works the Way It Does

在进化过程中，在功能上特征良好的顺式调控模块中发生的序列差异将被研究，以揭示这一信息丰富的基因组片段的变化规律。现在存在一套已知的非脊索动物后口动物物种和功能特征候选基因的文库，这些文库组成了有史以来最全面的实验平台之一，以解决这些问题。与参考物种相比，这6个可比物种的分化时间跨度为2000万年至5.4亿年。候选基因之前已经通过参考物种的基因转移进行了分析，并且已经开发了实验和计算工具来进行这些比较研究。将从8个候选基因中收集不同进化距离下的顺式调控模块序列。将对这些进行比较，以衡量发生的变化的质量和数量，并使用参考物种中的大插入重组报告结构的基因转移来验证其功能。除了支持顺式调控模块序列进化理论外，从这些机制中产生的规则将为发现基因组中的顺式调控模块提供更好的预测方法，因为以前的实验数据很少。更广泛的影响理解顺式调控模块如何进化是现代生物学中几个主要问题的联系。这里运作的机制将帮助我们解释基因组是如何工作的，发育是如何工作的，以及进化是如何工作的。在这里学到的原则的应用将通过通常的学术渠道传播，包括期刊出版物、会议报告、研究生和本科生教学以及书籍。PI和Co-PI有通过加州理工学院夏季本科生研究奖学金（SURF）让本科生参与实验室研究的历史，这些奖学金通常由REU对NSF拨款的补充资助。此外，PI定期在SURF特别审查委员会任职。研究生和博士后人员的培训是戴维森实验室、计算调控基因组学中心和基因组设施运作的重要组成部分。

Intellectual Merit The sequence differences that have occurred in functionally well characterized cis-regulatory modules over the course of evolution will be examined in order to reveal the rules of change in this information-rich segment of the genome. There now exists a set of libraries from well known non-chordate deuterostome species and functionally characterized candidate genes which comprise one of the most comprehensive experimental platforms ever assembled to address these questions. Compared to the reference species Strongylocentrotus purpuratus, the six comparable species' divergence times span from 20 to 540 million years. Candidate genes have been previously analyzed by gene transfer in the reference species and experimental and computational tools have been developed to undertake these comparative studies. From 8 candidates will be gathered the sequences of putative cis-regulatory modules at varying evolutionary distances. These will be compared to gauge the quality and quantity of changes that have occurred and their function will be verified using gene transfer of large-insert recombinant reporter constructs in the reference species. Besides supporting a theory of cis-regulatory module sequence evolution, the rules that emerge from these mechanisms will provide better predictive methods for discovering cis-regulatory modules in genomes where little previous experimental data is available. Broader Impacts Understanding how cis-regulatory modules evolve lies at the nexus of several major questions in modern biology. The mechanisms operating here will help explain us how the genome works, how development works and how evolution works. The application of the principles learned here will be disseminated through the usual academic channels including journal publications, meeting presentations, graduate and undergradate teaching, and books. The PI and Co-PI have a history of involving undergraduates in laboratory research through the Caltech Summer Undergraduate Research Fellowships (SURF), often funded by REU supplements to NSF grants. Additionally, the PI routinely serves on SURF ad hoc review boards. The training of graduate and post-doctoral personnel is an important component of the operation of the Davidson Laboratory, the Center for Computational Regulatory Genomics and the Genome Facility.