Solving a Bottleneck in Functional Genomics: Rules for Efficient Computational Identification of Cis-Regulatory Elements by Interspecific Sequence Comparison

解决功能基因组学的瓶颈：通过种间序列比较有效计算识别顺式调控元件的规则

• 批准号: 0212869
• 负责人: R. Andrew Cameron
• 金额: $ 93.91万
• 依托单位: California Institute of Technology
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-09-01 至 2006-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0212869&HistoricalAwards=false
• 关键词: Solving; Bottleneck; Functional; Genomics; Rules

0212869CameronUnderstanding the details of how individual cis-regulatory elements function and how the gene regulatory networks they form control developmental process is crucial to understanding how the genome works, how development works, and how evolution works. An effective method of locating individual cis-regulatory elements is comparative sequence analysis conducted at appropriate divergence times to reveal conserved elements. Current results show that this approach may yield a more than 10-fold increase in rate of experimental cis-regulatory element discovery, compared to the most efficient "blind" search methods. However, general rules for carrying out such analyses are not yet known, and initial work has shown very different degrees of similarity between genomic regions surrounding different genes in a single pair of sea urchin species. These investigators propose to determine the rules for efficient cis-regulatory sequence prediction by interspecific sequence analysis. To this end they will analyze and then test by gene transfer putative cis-regulatory elements identified in the vicinity of about 20 different genes, using several different echinoderm species that display a range of phylogenetic relatedness. The sea urchin embryo is a model system of choice in which this method can be quickly and effectively explored: species separated by various known evolutionary distances are available; they have already established methods for comparative prediction of conserved cis-regulatory sequence for one sea urchin species pair and shown that the methods work; and there is a practical high throughput gene transfer technology available. These investigators will construct BAC libraries for 6-8 species including sea urchins, and for more distant comparisons, a sea star and a hemichordate. Sequence of BACs containing the set of genes to be studied will be obtained, and they will then identify putative cis-regulatory regions for the candidate genes selected, as indicated by interspecific sequence comparison at diverse distances. These DNA fragments will be tested for cis-regulatory capability by gene transfer. Not only will this approach reveal rules for computational cis-regulatory analysis, but it will also support the extension of the current repertoire of BAC libraries, improve computational tools, and generate more efficient laboratory methods for this essential research area.

了解单个顺式调控元件如何发挥作用以及它们形成的基因调控网络如何控制发育过程的细节，对于理解基因组如何工作、发育如何工作以及进化如何工作至关重要。定位单个顺式调控元件的有效方法是在适当的发散时间进行比较序列分析，以揭示保守元件。目前的结果表明，与最有效的“盲”搜索方法相比，这种方法可能会使实验顺式调控元件的发现率增加10倍以上。然而，进行这种分析的一般规则尚不清楚，初步工作表明，在一对海胆物种中，不同基因周围的基因组区域之间的相似性程度非常不同。这些研究者建议通过种间序列分析来确定有效的顺式调控序列预测规则。为此，他们将分析并通过基因转移测试在大约20个不同基因附近发现的假定的顺式调节元件，使用几种不同的棘皮动物物种，这些物种显示出一系列的系统发育亲缘关系。海胆胚胎是一个选择的模型系统，在这个系统中，这种方法可以快速有效地探索：由各种已知进化距离分开的物种是可用的；他们已经建立了一种海胆物种对保守顺式调控序列的比较预测方法，并表明该方法有效；目前已有一种实用的高通量基因转移技术。这些研究人员将为包括海胆在内的6-8个物种建立BAC文库，并为更远的物种建立海星和半海胆。将获得包含待研究基因集的BACs序列，然后通过不同距离的种间序列比较，确定所选候选基因的假定顺式调控区域。这些DNA片段将通过基因转移测试顺式调控能力。这种方法不仅揭示了计算顺式调控分析的规则，而且还将支持扩展当前BAC库的曲目，改进计算工具，并为这一重要研究领域产生更有效的实验室方法。