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

0212869卡梅隆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。 一个有效的方法来定位个别顺式调控元件进行比较序列分析，在适当的分歧时间，以揭示保守的元素。 目前的研究结果表明，这种方法可能会产生超过10倍的增加率的实验顺式调控元件的发现，相比，最有效的“盲”搜索方法。 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，围绕不同基因的基因组区域之间存在非常不同程度的相似性。 这些研究人员建议，以确定有效的顺式调控序列预测的种间序列分析的规则。 为此，他们将使用几种不同的棘皮动物物种，通过基因转移分析并测试在大约20个不同基因附近鉴定的推定顺式调控元件，这些棘皮动物物种显示出一系列系统发育相关性。 海胆胚胎是一个模型系统的选择，这种方法可以快速有效地探索：物种分离的各种已知的进化距离是可用的;他们已经建立了方法比较预测保守的顺式调控序列的一个海胆物种对，并表明该方法的工作;有一个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个物种构建BAC文库，并为更远的比较构建一个海星星星和一个半索动物。 将获得包含待研究基因组的BAC序列，然后将鉴定所选候选基因的推定顺式调控区，如不同距离处的种间序列比较所示。 将通过基因转移检测这些DNA片段的顺式调节能力。 这种方法不仅将揭示计算顺式调节分析的规则，而且还将支持扩展当前的BAC库库，改进计算工具，并为这一重要研究领域生成更有效的实验室方法。

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.