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

智力优势在进化过程中，在功能上具有良好特征的顺式调控模块中发生的序列差异将被检查，以揭示基因组中这个信息丰富的片段的变化规则。 现在存在一组来自众所周知的非脊索动物后口动物物种和功能特征的候选基因的文库，其包括有史以来组装以解决这些问题的最全面的实验平台之一。与参考物种Strongylocentrotus purpuratus相比，6个可比物种的分歧时间从2000万年到5.4亿年不等。 候选基因已在参考物种中通过基因转移进行了分析，并开发了实验和计算工具来进行这些比较研究。 从8个候选者中收集不同进化距离的推定顺式调控模块的序列。将对这些进行比较，以衡量已发生变化的质量和数量，并使用参考种属中大插入重组报告基因构建体的基因转移验证其功能。 除了支持顺式调控模块序列进化的理论，从这些机制中出现的规则将提供更好的预测方法，发现基因组中的顺式调控模块，以前的实验数据很少。 了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核心。 这里的运作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，进化是如何工作的。 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，会议演示，研究生和本科生教学和书籍。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，该奖学金通常由REU补充NSF赠款资助。 此外，主要研究员还经常担任分区域资源中心特设审查委员会的成员。 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.